[Freesurfer] Projection of CBF maps on fsaverage and smooth

[Matthieu Vanhoutte]

Dear Freesurfer's experts,

I computed some perfusion maps from ASL data. These perfusion maps were 
registered on anatomical T1 and I would like to make a group analysis on 
surfaces. Please find below my actual commands in order to project these 
volumic maps on fsaverage then smooth the data projected on fsaverage :


*Project CBF maps on fsaverage* :
/mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject fsaverage 
--interp trilin --projfrac 0.5 --hemi lh --o lh.fsaverage.cbf.mgh 
--noreshape --cortex --surfreg sphere.reg//
//mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject 
fsaverage --interp trilin --projfrac 0.5 --hemi rh --o 
rh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg/


*Smooth the data projected on fsaverage (native ASL data size voxel of 
3mm)* :
/mris_fwhm --s fsaverage --hemi lh --smooth-only --i 
lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask 
brain.fsaverage.lh.mgh//
//mris_fwhm --s fsaverage --hemi rh --smooth-only --i 
rh.fsaverage.cbf.mgh --fwhm 3 --o rh.fwhm3.fsaverage.cbf.mgh --mask 
brain.fsaverage.rh.mgh/


Could you advise me on these two steps and tell me first if this is the 
best way to project CBF maps on fsaverage, then to smooth the data on 
surfaces ? Is my process could be improved ?


Best regards,

--
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

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Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Matthieu Vanhoutte]

Dear Doug,

Thank you for helping !

Yes I directly used the regheader option because in the steps before I
already registered ASL maps on anatomical T1.

The brain.fsaverage.lh.mgh come from the projection of the T1 brain mask
(dilated by 1) on the fsaverage.

1) So isn't it better to project first on the anatomical subject then on
fsaverage than what I've done ?

2) Smoothing with mris_fwhm is a good way with --mask option ?

Thank you for your precious advices !

Best regards,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-03-01 19:45 GMT+01:00 Douglas Greve :

>
> Basically looks ok. The only things that jump out at me are that you are
> using regheader (I would create a registration file with bbregister rather
> than assuming that there was no motion between the anatomical and the ASL).
> Where did brain.fsaverage.lh.mgh come from?
> doug
>
>
>
> On 2/27/15 2:16 PM, Matthieu Vanhoutte wrote:
>
> Dear Freesurfer's experts,
>
> I computed some perfusion maps from ASL data. These perfusion maps were
> registered on anatomical T1 and I would like to make a group analysis on
> surfaces. Please find below my actual commands in order to project these
> volumic maps on fsaverage then smooth the data projected on fsaverage :
>
> *Project CBF maps on fsaverage* :
> *mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject fsaverage
> --interp trilin --projfrac 0.5 --hemi lh --o lh.fsaverage.cbf.mgh
> --noreshape --cortex --surfreg sphere.reg*
> *mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject fsaverage
> --interp trilin --projfrac 0.5 --hemi rh --o rh.fsaverage.cbf.mgh
> --noreshape --cortex --surfreg sphere.reg*
>
> *Smooth the data projected on fsaverage (native ASL data size voxel of
> 3mm)* :
> *mris_fwhm --s fsaverage --hemi lh --smooth-only --i lh.fsaverage.cbf.mgh
> --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask brain.fsaverage.lh.mgh*
> *mris_fwhm --s fsaverage --hemi rh --smooth-only --i rh.fsaverage.cbf.mgh
> --fwhm 3 --o rh.fwhm3.fsaverage.cbf.mgh --mask brain.fsaverage.rh.mgh*
>
> Could you advise me on these two steps and tell me first if this is the
> best way to project CBF maps on fsaverage, then to smooth the data on
> surfaces ? Is my process could be improved ?
>
> Best regards,
>
> --
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
>
>
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>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Matthieu Vanhoutte]

Thank you Doug for precisely helping me on smooth detailed command.

Concerning projection on fsaverage, is it better, worse or equivalent to do
(1) or (2) ?

(1)

*# Project and smooth onto anatomical surface* (--surf mid : mean surface
between pial and white)

*mri_vol2surf --mov **cbf.nii.gz --hemi lh --surf mid --o lh.fwhm3.cbf.w
--regheader *

*subj_id --out_type paint --surf-fwhm 3mris_w_to_curv **subj_id lh
**lh.fwhm3.cbf.w
*







*lh.fwhm3.cbfmv ${DIR}/surf/lh.fwhm${FWHM}.intensity
${DIR}/ictus/lh.fwhm${FWHM}.intensityrm -f
${DIR}/surf/lh.fwhm${FWHM}.intensity.w# Resample cbf to fsaverage
mri_surf2surf --srcsubject **subj_id --srchemi lh --srcsurfreg sphere.reg
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --sval
**lh.fwhm3.cbf
--sfmt curv --noreshape --no-cortex --tval lh.fwhm3.fsaverage.cbf.mgh
--tfmt curv*


(2)

*# Project and smooth onto fsaverage*
*mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject fsaverage
--interp trilin --projfrac 0.5 --hemi lh --o lh.fsaverage.cbf.mgh
--noreshape --cortex --surfreg sphere.reg*

*# Smooth*
*mris_fwhm --s fsaverage --hemi lh --smooth-only --i lh.fsaverage.cbf.mgh
--fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask brain.fsaverage.lh.mgh*


Many thanks in advance !!

Best regards,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-03-02 21:13 GMT+01:00 Douglas N Greve :

>
> On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> > Dear Doug,
> >
> > Thank you for helping !
> >
> > Yes I directly used the regheader option because in the steps before I
> > already registered ASL maps on anatomical T1.
> >
> > The brain.fsaverage.lh.mgh come from the projection of the T1 brain
> > mask (dilated by 1) on the fsaverage.
> >
> > 1) So isn't it better to project first on the anatomical subject then
> > on fsaverage than what I've done ?
> This is what is done internally when you spec a target subject that is
> not the same as the source subject.
> >
> > 2) Smoothing with mris_fwhm is a good way with --mask option ?
> Yes, though I don't think that masking will have an effect the way you
> created the mask (everything will be in the mask). I would use --cortex
> to smooth only within cortex (and so exclude the medial wall).
> doug
>
> >
> > Thank you for your precious advices !
> >
> > Best regards,
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> > 2015-03-01 19:45 GMT+01:00 Douglas Greve  > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> >
> > Basically looks ok. The only things that jump out at me are that
> > you are using regheader (I would create a registration file with
> > bbregister rather than assuming that there was no motion between
> > the anatomical and the ASL). Where did brain.fsaverage.lh.mgh come
> > from?
> > doug
> >
> >
> >
> > On 2/27/15 2:16 PM, Matthieu Vanhoutte wrote:
> >> Dear Freesurfer's experts,
> >>
> >> I computed some perfusion maps from ASL data. These perfusion
> >> maps were registered on anatomical T1 and I would like to make a
> >> group analysis on surfaces. Please find below my actual commands
> >> in order to project these volumic maps on fsaverage then smooth
> >> the data projected on fsaverage :
> >>
> >> *Project CBF maps on fsaverage* :
> >> /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
> >> fsaverage --interp trilin --projfrac 0.5 --hemi lh --o
> >> lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg//
> >> //mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
> >> fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
> >> rh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg/
> >>
> >> *Smooth the data projected on fsaverage (native ASL data size
> >> voxel of 3mm)* :
> >> /mris_fwhm --s fsaverage --hemi lh --smooth-only --i
> >> lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh
> >> --mask brain.fsaverage.lh.mgh//
> >> //mris_fwhm --s fsaverage --hemi rh --smooth-only --i
> >> rh.fsaverage.cbf.mgh --fwhm 3 --o rh.fwhm3.fsaverage.cbf.mgh
> >> --mask brain.fsaverage.rh.mgh/
> >>
> >> Could you advise me on these two steps and tell me first if this
> >> is the best way to

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Matthieu Vanhoutte]

*Update from precedent mail*

Concerning projection on fsaverage, is it better, worse or equivalent to do
(1) or (2) ?

(1)

*# Project and smooth onto anatomical surface* (--surf mid : mean surface
between pial and white)

*mri_vol2surf --mov **cbf.nii.gz --hemi lh --surf mid --o lh.fwhm3.cbf.w
--regheader *

*subj_id --out_type paint --surf-fwhm 3mris_w_to_curv **subj_id lh
**lh.fwhm3.cbf.w
*



*lh.fwhm3.cbf# Resample cbf to fsaverage   mri_surf2surf --srcsubject **subj_id
--srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh
--trgsurfreg sphere.reg --sval **lh.fwhm3.cbf --sfmt curv --noreshape
--no-cortex --tval lh.fwhm3.fsaverage.cbf.mgh --tfmt curv*


(2)

*# Project and smooth onto fsaverage*
*mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject fsaverage
--interp trilin --projfrac 0.5 --hemi lh --o lh.fsaverage.cbf.mgh
--noreshape --cortex --surfreg sphere.reg*

*# Smooth*
*mris_fwhm --s fsaverage --hemi lh --smooth-only --i lh.fsaverage.cbf.mgh
--fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask brain.fsaverage.lh.mgh*


Many thanks in advance !!

Best regards,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-03-05 14:10 GMT+01:00 Matthieu Vanhoutte :

> Thank you Doug for precisely helping me on smooth detailed command.
>
> Concerning projection on fsaverage, is it better, worse or equivalent to
> do (1) or (2) ?
>
> (1)
>
> *# Project and smooth onto anatomical surface* (--surf mid : mean surface
> between pial and white)
>
> *mri_vol2surf --mov **cbf.nii.gz --hemi lh --surf mid --o lh.fwhm3.cbf.w
> --regheader *
>
> *subj_id --out_type paint --surf-fwhm 3mris_w_to_curv **subj_id lh 
> **lh.fwhm3.cbf.w
> *
>
>
>
>
>
>
>
> *lh.fwhm3.cbfmv ${DIR}/surf/lh.fwhm${FWHM}.intensity
> ${DIR}/ictus/lh.fwhm${FWHM}.intensityrm -f
> ${DIR}/surf/lh.fwhm${FWHM}.intensity.w# Resample cbf to fsaverage
> mri_surf2surf --srcsubject **subj_id --srchemi lh --srcsurfreg sphere.reg
> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --sval 
> **lh.fwhm3.cbf
> --sfmt curv --noreshape --no-cortex --tval lh.fwhm3.fsaverage.cbf.mgh
> --tfmt curv*
>
>
> (2)
>
> *# Project and smooth onto fsaverage*
> *mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject fsaverage
> --interp trilin --projfrac 0.5 --hemi lh --o lh.fsaverage.cbf.mgh
> --noreshape --cortex --surfreg sphere.reg*
>
> *# Smooth*
> *mris_fwhm --s fsaverage --hemi lh --smooth-only --i lh.fsaverage.cbf.mgh
> --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask brain.fsaverage.lh.mgh*
>
>
> Many thanks in advance !!
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-03-02 21:13 GMT+01:00 Douglas N Greve :
>
>>
>> On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
>> > Dear Doug,
>> >
>> > Thank you for helping !
>> >
>> > Yes I directly used the regheader option because in the steps before I
>> > already registered ASL maps on anatomical T1.
>> >
>> > The brain.fsaverage.lh.mgh come from the projection of the T1 brain
>> > mask (dilated by 1) on the fsaverage.
>> >
>> > 1) So isn't it better to project first on the anatomical subject then
>> > on fsaverage than what I've done ?
>> This is what is done internally when you spec a target subject that is
>> not the same as the source subject.
>> >
>> > 2) Smoothing with mris_fwhm is a good way with --mask option ?
>> Yes, though I don't think that masking will have an effect the way you
>> created the mask (everything will be in the mask). I would use --cortex
>> to smooth only within cortex (and so exclude the medial wall).
>> doug
>>
>> >
>> > Thank you for your precious advices !
>> >
>> > Best regards,
>> >
>> > -
>> > Matthieu Vanhoutte, MSc
>> > Research Engineer - Department of Neuroradiology
>> > Regional University Hospital, Lille, France
>> >
>> > 2015-03-01 19:45 GMT+01:00 Douglas Greve > > <mailto:gr...@nmr.mgh.harvard.edu>>:
>> >
>> >
>> > Basically looks ok. The only things that jump out at me are that
>> > you are using regheader (I would create a registration file with
>> > bbregister rather than assuming that there was no motion between
>> > the anatomical and the ASL). Where did brain.fsaverage.lh.mgh come
>> > from?
>> >

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Matthieu Vanhoutte]

Thank you Douglas but I don't understand the solution you propose. Could
you please show me the command lines ?

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-03-05 16:45 GMT+01:00 Douglas N Greve :

>
>
> #1 is probably better. BTW, why are you changing format from w to curv?
> Why use curv at all? I'd use mgz or nifti.
>
>
>
> On 03/05/2015 08:10 AM, Matthieu Vanhoutte wrote:
> > Thank you Doug for precisely helping me on smooth detailed command.
> >
> > Concerning projection on fsaverage, is it better, worse or equivalent
> > to do (1) or (2) ?
> >
> > (1)
> >
> > */# Project and smooth onto anatomical surface/* (--surf mid : mean
> > surface between pial and white)
> >
> > /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o
> > lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint --surf-fwhm 3
> >
> > mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/ lh.fwhm3.cbf//
> >
> > mv ${DIR}/surf/lh.fwhm${FWHM}.intensity
> > ${DIR}/ictus/lh.fwhm${FWHM}.intensity
> >
> > rm -f ${DIR}/surf/lh.fwhm${FWHM}.intensity.w
> >
> > *# Resample cbf to fsaverage*
> >
> > mri_surf2surf --srcsubject /subj_id/// --srchemi lh --srcsurfreg
> > sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg
> > --sval /lh.fwhm3.cbf/// --sfmt curv --noreshape --no-cortex --tval
> > lh.fwhm3.fsaverage.cbf.mgh --tfmt curv/
> >
> >
> > (2)
> >
> > */# Project and smooth onto fsaverage/*
> > /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
> > fsaverage --interp trilin --projfrac 0.5 --hemi lh --o
> > lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg//
> > /
> > */# Smooth/*
> > /mris_fwhm --s fsaverage --hemi lh --smooth-only --i
> > lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask
> > brain.fsaverage.lh.mgh//
> > /
> >
> > Many thanks in advance !!
> >
> > Best regards,
> >
> > -----
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> > 2015-03-02 21:13 GMT+01:00 Douglas N Greve  > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> >
> > On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> > > Dear Doug,
> > >
> > > Thank you for helping !
> > >
> > > Yes I directly used the regheader option because in the steps
> > before I
> > > already registered ASL maps on anatomical T1.
> > >
> > > The brain.fsaverage.lh.mgh come from the projection of the T1 brain
> > > mask (dilated by 1) on the fsaverage.
> > >
> > > 1) So isn't it better to project first on the anatomical subject
> > then
> > > on fsaverage than what I've done ?
> > This is what is done internally when you spec a target subject that
> is
> > not the same as the source subject.
> > >
> > > 2) Smoothing with mris_fwhm is a good way with --mask option ?
> > Yes, though I don't think that masking will have an effect the way
> you
> > created the mask (everything will be in the mask). I would use
> > --cortex
> > to smooth only within cortex (and so exclude the medial wall).
> > doug
> >
> > >
> > > Thank you for your precious advices !
> > >
> > > Best regards,
> > >
> > > -
> > > Matthieu Vanhoutte, MSc
> > > Research Engineer - Department of Neuroradiology
> > > Regional University Hospital, Lille, France
> > >
> > > 2015-03-01 19:45 GMT+01:00 Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>>:
> > >
> > >
> > > Basically looks ok. The only things that jump out at me are
> that
> > > you are using regheader (I would create a registration file
> with
> > > bbregister rather than assuming that there was no motion
> between
> > > the anatomical and the ASL). Where did
> > brain.fsaverage.lh.mgh come
> > > from?
> > > doug
> > >
> > >
> >  

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Matthieu Vanhoutte]

I don't know if we are talking about the same thing.

In precedent mail you told me solution #1 was better :

*# Project and smooth onto anatomical surface* (--surf mid : mean surface
between pial and white)

*mri_vol2surf --mov **cbf.nii.gz --hemi lh --surf mid --o lh.fwhm3.cbf.w
--regheader *

*subj_id --out_type paint --surf-fwhm 3mris_w_to_curv **subj_id lh
**lh.fwhm3.cbf.w
*



*lh.fwhm3.cbf# Resample cbf to fsaverage   mri_surf2surf --srcsubject **subj_id
--srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh
--trgsurfreg sphere.reg --sval *


*lh.fwhm3.cbf --sfmt curv --noreshape --no-cortex --tval
lh.fwhm3.fsaverage.cbf.mgh --tfmt curv*
But you told me :



*BTW, why are you changing format from w to curv? Why use curv at all? I'd
use mgz or nifti.*
At this point I don't know what this means ?

Thanks,

Matthieu

2015-03-05 17:12 GMT+01:00 Douglas N Greve :

>
> Just add --trgsubject fsaverage to the mri_vol2surf command line. Run
> mri_vol2surf with --help to get more info
>
> On 03/05/2015 10:52 AM, Matthieu Vanhoutte wrote:
> > Thank you Douglas but I don't understand the solution you propose.
> > Could you please show me the command lines ?
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> > 2015-03-05 16:45 GMT+01:00 Douglas N Greve  > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> >
> >
> > #1 is probably better. BTW, why are you changing format from w to
> > curv?
> > Why use curv at all? I'd use mgz or nifti.
> >
> >
> >
> > On 03/05/2015 08:10 AM, Matthieu Vanhoutte wrote:
> > > Thank you Doug for precisely helping me on smooth detailed command.
> > >
> > > Concerning projection on fsaverage, is it better, worse or
> > equivalent
> > > to do (1) or (2) ?
> > >
> > > (1)
> > >
> > > */# Project and smooth onto anatomical surface/* (--surf mid : mean
> > > surface between pial and white)
> > >
> > > /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o
> > > lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint
> > --surf-fwhm 3
> > >
> > > mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/
> > lh.fwhm3.cbf//
> > >
> > > mv ${DIR}/surf/lh.fwhm${FWHM}.intensity
> > > ${DIR}/ictus/lh.fwhm${FWHM}.intensity
> > >
> > > rm -f ${DIR}/surf/lh.fwhm${FWHM}.intensity.w
> > >
> > > *# Resample cbf to fsaverage*
> > >
> > > mri_surf2surf --srcsubject /subj_id/// --srchemi lh
> --srcsurfreg
> > > sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg
> sphere.reg
> > > --sval /lh.fwhm3.cbf/// --sfmt curv --noreshape --no-cortex
> > --tval
> > > lh.fwhm3.fsaverage.cbf.mgh --tfmt curv/
> > >
> > >
> > > (2)
> > >
> > > */# Project and smooth onto fsaverage/*
> > > /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
> > > fsaverage --interp trilin --projfrac 0.5 --hemi lh --o
> > > lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg//
> > > /
> > > */# Smooth/*
> > > /mris_fwhm --s fsaverage --hemi lh --smooth-only --i
> > > lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask
> > > brain.fsaverage.lh.mgh//
> >     > /
> > >
> > > Many thanks in advance !!
> > >
> > > Best regards,
> > >
> > > -
> > > Matthieu Vanhoutte, MSc
> > > Research Engineer - Department of Neuroradiology
> > > Regional University Hospital, Lille, France
> > >
> > > 2015-03-02 21:13 GMT+01:00 Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>>:
> > >
> > >
> > > On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> > > > Dear Doug,
> > > >
> > > > Thank you for helping !
> > > >
> > > > Yes I directly used the regheader option because in the steps
> > > before I
> > > > already registered ASL maps on anatomical 

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Matthieu Vanhoutte]

Ok, thanks.

Then is this command below summarise the best for project on fsaverage and
smooth, according to our mails exchange :

*mri_vol2surf --mov **cbf.nii.gz --hemi lh --surf mid --o
**lh.fwhm3.fsaverage.cbf.mgh
--regheader **subj_id --surf-fwhm 3* --trgsubject fsaverage --icoorder 7
--cortex

Best regards,


-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-03-05 17:24 GMT+01:00 Douglas N Greve :

> w format is the paint format output from your vol2surf command. We tend
> not to use either w or curv formats anymore
> On 03/05/2015 11:19 AM, Matthieu Vanhoutte wrote:
> > I don't know if we are talking about the same thing.
> >
> > In precedent mail you told me solution #1 was better :
> >
> > */# Project and smooth onto anatomical surface/* (--surf mid : mean
> > surface between pial and white)
> >
> > /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o
> > lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint --surf-fwhm 3
> >
> > mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/ lh.fwhm3.cbf//
> >
> > *# Resample cbf to fsaverage*
> >
> > mri_surf2surf --srcsubject /subj_id/// --srchemi lh --srcsurfreg
> > sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg
> > --sval /lh.fwhm3.cbf/// --sfmt curv --noreshape --no-cortex --tval
> > lh.fwhm3.fsaverage.cbf.mgh --tfmt curv
> >
> >
> > /
> > But you told me :
> > /BTW, why are you changing format from w to curv?
> > Why use curv at all? I'd use mgz or nifti.
> >
> > /
> > At this point I don't know what this means ?
> >
> > Thanks,
> >
> > Matthieu
> >
> > 2015-03-05 17:12 GMT+01:00 Douglas N Greve  > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> >
> > Just add --trgsubject fsaverage to the mri_vol2surf command line. Run
> > mri_vol2surf with --help to get more info
> >
> >     On 03/05/2015 10:52 AM, Matthieu Vanhoutte wrote:
> > > Thank you Douglas but I don't understand the solution you propose.
> > > Could you please show me the command lines ?
> > >
> > > -
> > > Matthieu Vanhoutte, MSc
> > > Research Engineer - Department of Neuroradiology
> > > Regional University Hospital, Lille, France
> > >
> > > 2015-03-05 16:45 GMT+01:00 Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>>:
> > >
> > >
> > >
> > > #1 is probably better. BTW, why are you changing format from
> > w to
> > > curv?
> > > Why use curv at all? I'd use mgz or nifti.
> > >
> > >
> > >
> > > On 03/05/2015 08:10 AM, Matthieu Vanhoutte wrote:
> > > > Thank you Doug for precisely helping me on smooth detailed
> > command.
> > > >
> > > > Concerning projection on fsaverage, is it better, worse or
> > > equivalent
> > > > to do (1) or (2) ?
> > > >
> > > > (1)
> > > >
> > > > */# Project and smooth onto anatomical surface/* (--surf
> > mid : mean
> > > > surface between pial and white)
> > > >
> > > > /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o
> > > > lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint
> > > --surf-fwhm 3
> > > >
> > > > mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/
> > > lh.fwhm3.cbf//
> > > >
> > > > mv ${DIR}/surf/lh.fwhm${FWHM}.intensity
> > > > ${DIR}/ictus/lh.fwhm${FWHM}.intensity
> > > >
> > > > rm -f ${DIR}/surf/lh.fwhm${FWHM}.intensity.w
> > > >
> > > > *# Resample cbf to fsaverage*
> > > >
> > > > mri_surf2surf --srcsubject /subj_id/// --srchemi lh
> > --srcsurfreg
> > > > sphere.reg --trgsubject fsaverage --trghemi lh
> > --trgsurfreg sphere.reg
> > > > --sval /lh.fwhm3.cbf/// --sfmt c

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Matthieu Vanhoutte]

Thanks !

Why remove icoorder because it was suggested in the mri_vol2surf --help
examples ?

May I ask you a last question : I want to make a group analyse with
freesurfer tools. With these CBF projected on fsaverage and smooth (with
the last command line), could I do as if my data were previously cached
(qcached) and use the "mri_preproc --cache-in" command ?

Best regards,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-03-05 18:02 GMT+01:00 Douglas N Greve :

> yes, but remove icoorder
>
> On 03/05/2015 11:50 AM, Matthieu Vanhoutte wrote:
> > Ok, thanks.
> >
> > Then is this command below summarise the best for project on fsaverage
> > and smooth, according to our mails exchange :
> >
> > /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o
> > //lh.fwhm3.fsaverage.cbf.mgh --regheader ///subj_id/ --surf-fwhm 3/
> > --trgsubject fsaverage --icoorder 7 --cortex
> >
> > Best regards,
> >
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> > 2015-03-05 17:24 GMT+01:00 Douglas N Greve  > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> > w format is the paint format output from your vol2surf command. We
> > tend
> > not to use either w or curv formats anymore
> > On 03/05/2015 11:19 AM, Matthieu Vanhoutte wrote:
> > > I don't know if we are talking about the same thing.
> > >
> > > In precedent mail you told me solution #1 was better :
> > >
> > > */# Project and smooth onto anatomical surface/* (--surf mid : mean
> > > surface between pial and white)
> > >
> > > /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o
> > > lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint
> > --surf-fwhm 3
> > >
> > > mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/
> > lh.fwhm3.cbf//
> > >
> > > *# Resample cbf to fsaverage*
> > >
> > > mri_surf2surf --srcsubject /subj_id/// --srchemi lh
> --srcsurfreg
> > > sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg
> > sphere.reg
> > > --sval /lh.fwhm3.cbf/// --sfmt curv --noreshape --no-cortex
> > --tval
> > > lh.fwhm3.fsaverage.cbf.mgh --tfmt curv
> > >
> > >
> > > /
> > > But you told me :
> > > /BTW, why are you changing format from w to curv?
> > > Why use curv at all? I'd use mgz or nifti.
> > >
> > > /
> > > At this point I don't know what this means ?
> > >
> > > Thanks,
> > >
> > > Matthieu
> > >
> > > 2015-03-05 17:12 GMT+01:00 Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>>:
> > >
> > >
> > > Just add --trgsubject fsaverage to the mri_vol2surf command
> > line. Run
> > > mri_vol2surf with --help to get more info
> > >
> > > On 03/05/2015 10:52 AM, Matthieu Vanhoutte wrote:
> > > > Thank you Douglas but I don't understand the solution you
> > propose.
> > > > Could you please show me the command lines ?
> > > >
> > > > -
> > > > Matthieu Vanhoutte, MSc
> > > > Research Engineer - Department of Neuroradiology
> > > > Regional University Hospital, Lille, France
> > > >
> > > > 2015-03-05 16:45 GMT+01:00 Douglas N Greve
> > >  > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
> >>
> > > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>>>:
> > > >
> > > >
> > > >
> > > > #1 is probably better. BTW, why are you changing
> > format from
> > > w to
> > > >

Re: [Freesurfer] GLM analysis on CBF maps

[Matthieu Vanhoutte]

Hello,

I have run GLM group analyses with Freesurfer tools according DODS model,
with six classes ((Male,Female) ; (Control,Left,Right)) and one age
variable :







*Class MaleControlClass MaleLeftClass MaleRightClass FemaleControlClass
FemaleLeftClass FemaleRightVariables Age *

I wanted to test *Control > Left* and *Control > Right* on CBF maps. I
defined with help of the tutorial contrats for that :




*control-left.intercept.mtx : 0.5 -0.5 0 0.5 -0.5 0 0 0 0 0 0
0control-left.slope.mtx : 0 0 0 0 0 0 0.5 -0.5 0 0.5 -0.5
0control-right.intercept.mtx : 0.5 0 -0.5 0.5 0 -0.5 0 0 0 0 0
0control-right.slope.mtx : 0 0 0 0 0 0 0.5 0 -0.5 0.5 0 -0.5*

My problem is that I don't know how to interpret significative results in
both *Control > Left *contrasts* : **control-left.intercept.mtx *and
*control-left.slope.mtx.
*The same for* Control > Right.* One is coding for intercept and the other
for slope, but concretely what significative results in both contrasts mean
?

Thank you in advance for helping !

Best regards,

-----
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-03-11 16:51 GMT+01:00 Douglas N Greve :

>
> the sig value is actually  -log10(p)*sign(gamma) where gamma is the
> contrast (gamma.mgh). The p-value is two-tailed, and the color indicates
> what tail you are on.
> doug
>
> On 03/10/2015 01:21 PM, Matthieu Vanhoutte wrote:
> > Dear FreeSurfer's experts,
> >
> > I have launched a GLM analyses following the tutorial :
> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> >
> > Below the command I have used :
> >
> > /mri_glmfit \
> >   --y
> >
> ${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.all.subjects.fwhm3.fsaverage.cbf_s.mgh
> > \
> >   --fsgd ${FS_DIR}/SurfaceAnalysis_mri_glmfit/g6v1.fsgd dods \
> >   --C ${FS_DIR}/SurfaceAnalysis_mri_glmfit/control-left.intercept.mtx \
> >   --surf fsaverage lh \
> >   --cortex \
> >   --glmdir ${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/
> >
> >
> > In order to see the uncorrected results with p<.0001, I ran :
> >
> > /freeview -f
> >
> ${SUBJECTS_DIR}/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=${SUBJECTS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/control-left.intercept/sig.mgh:overlay_threshold=4,5
> > -viewport 3d/
> >
> > However, nothing appears with this threshold and when I wanted to
> > configure overlay I saw that most of my values in /sig.mgh /were
> > negatives between -4 and 0...
> >
> > How is possible for /-log10(pvalue)/ values ? Could I obtain
> > significant uncorrected values from this /sig.mgh/ file ?
> >
> > Please find attached my needed files : *y.fsgd, mri_glmfit.log,
> > **/control-left.intercept.mtx/ and sig.mgh *
> >
> > Thank you in advance for helping me !!
> >
> > Best regards,
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
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[Freesurfer] [FreeSurfer] mri_glmfit with fractional values in contrast file .mtx

[Matthieu Vanhoutte]

Dear experts,

Could you indicate me how to specify a contrast vector with fractional
values ? I tried the below formats without success in the .mtx file:

[0 0 0 0 0 0 1 1 1 -1 -1 -1]/3

|0 0 0 0 0 0 1 1 1 -1 -1 -1|/3

0 0 0 0 0 0 1/3 1/3 1/3 -1/3 -1/3 -1/3

Thank in advance for helping !

Best regards,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
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[Freesurfer] [FreeSurfer] Visualize & Compute Overlaps between two significant surface maps

[Matthieu Vanhoutte]

Dear FreeSurer's experts,

I used group analysis based on GLM to compute significative surface maps of
different characteristics : thickness, CBF,...

Now I've got these maps I would like to visualize overlaps between two
different maps and compute the overlap ratio.

How could I succeed these two steps ?

Best regards,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
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Re: [Freesurfer] [FreeSurfer] mri_glmfit with fractional values in contrast file .mtx

[Matthieu Vanhoutte]

Thank you Douglas.

Matthieu Vanhoutte, MSc
Research Engineer - Neuroradiology Department
Regional University Hospital, Lille, France
Le 16 mars 2015 18:17, "Douglas N Greve"  a
écrit :

> you'll need to use .33
>
> On 03/16/2015 11:09 AM, Matthieu Vanhoutte wrote:
> > Dear experts,
> >
> > Could you indicate me how to specify a contrast vector with fractional
> > values ? I tried the below formats without success in the .mtx file:
> >
> > [0 0 0 0 0 0 1 1 1 -1 -1 -1]/3
> >
> > |0 0 0 0 0 0 1 1 1 -1 -1 -1|/3
> >
> > 0 0 0 0 0 0 1/3 1/3 1/3 -1/3 -1/3 -1/3
> >
> > Thank in advance for helping !
> >
> > Best regards,
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] [FreeSurfer] Visualize & Compute Overlaps between two significant surface maps

[Matthieu Vanhoutte]

Thank you Douglas I will try this.

Matthieu Vanhoutte, MSc
Research Engineer - Neuroradiology Department
Regional University Hospital, Lille, France
Le 16 mars 2015 19:13, "Douglas N Greve"  a
écrit :

>
> For visualizing the overlap, I would probably create a segmentation in
> which each vertex is either 1 (present in thickness), 2 (present in
> CBF), or 3 present in both. You can do this in matlab or with a
> combination of mri_binarize and fscalc. You can then create an
> annotation from the seg with mris_seg2annot. I would compute a dice
> coefficent of the overlap in matlab, something like
>
> dice = n12/((n1+n2)/2)
>
> where n1 is the number of vetices in thick, n2 for cbf, and n12 is the
> number that overlap
>
> doug
>
> On 03/16/2015 12:09 PM, Matthieu Vanhoutte wrote:
> > Dear FreeSurer's experts,
> >
> > I used group analysis based on GLM to compute significative surface
> > maps of different characteristics : thickness, CBF,...
> >
> > Now I've got these maps I would like to visualize overlaps between two
> > different maps and compute the overlap ratio.
> >
> > How could I succeed these two steps ?
> >
> > Best regards,
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
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[Freesurfer] [FreeSurfer] : Convert asl data from fsaverage (surface) to MNI305 (volume)

[Matthieu Vanhoutte]

Dear experts,

I have some asl data on fsaverage surface and would like to compute them on
MNI305 volume. So I executed the commands below, but when merging left and
right hemispheres it seems that the *--fillribbon *option on
*MNI305.asl.nii.gz* output data didn't work for right hemisphere :



*mri_surf2vol --surfval lh.fsaverage.asl --fillribbon --identity fsaverage
--template fsaverage/mri/T1.mgz --hemi lh --o
lh.MNI305.asl.nii.gzmri_surf2vol --surfval rh.fsaverage.asl --fillribbon
--identity fsaverage --merge lh.MNI305.asl.nii.gz --hemi rh --o
MNI305.asl.nii.gz*

What should I have to do ?

Many thanks in advance for helping !

Best regards,

Matthieu
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Re: [Freesurfer] [FreeSurfer] : Convert asl data from fsaverage (surface) to MNI305 (volume)

[Matthieu Vanhoutte]

Hello Douglas,

I have download the new version of mri_surf2vol you supplied me, and have
copied it in the FS5.3 /bin installation files.

But when I tried to launch with my precedent command lines, the error
message appeared :






































*gdiagno = -1Using identity matrix for
registration--GNU
libc version: 2.19ERROR: Systems running GNU glibc version greater than
2.15  require a newly formatted license file (it's free). Please  download
a new one from the following page:
http://surfer.nmr.mgh.harvard.edu/registration.html
<http://surfer.nmr.mgh.harvard.edu/registration.html>--gdiagno
= -1Using merge volume as templateUsing identity matrix for
registrationniiRead(): error opening file
/home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI305.asl.nii.gzmri_surf2vol
ERROR: reading
/home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI305.asl.nii.gz
headerMatrix from regfile: 0.998  -0.007   0.018   0.957;-0.013  -0.009
0.997  -17.816;-0.015  -1.001   0.002  -18.550; 0.000   0.000   0.000
1.000;movvol /home/global//fsl50/data/standard/MNI152_T1_2mm.nii.gztargvol
/home/fatmike/sebastien/FS5.1/207020_T0/asl/MNI305.asl.nii.gzoutvol
/home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI152.asl.nii.gzregfile
/home/global//freesurfer5.3//average/mni152.register.datinvert 1tal
0talres 2regheader 0noresample 0interp  nearest (0)precision  float
(3)Gdiag_no  -1Synth  0SynthSeed  1427897150Invert!niiRead(): error
opening file /home/fatmike/sebastien/FS5.1/207020_T0/asl/MNI305.asl.nii.gz*

What shoul I do ?

Best regards,

Matthieu

2015-03-26 21:27 GMT+01:00 Douglas N Greve :

>
> That version had a bug. Try this version
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
>
> On 03/26/2015 12:16 PM, Matthieu Vanhoutte wrote:
> > Dear experts,
> >
> > I have some asl data on fsaverage surface and would like to compute
> > them on MNI305 volume. So I executed the commands below, but when
> > merging left and right hemispheres it seems that the /--fillribbon
> > /option on /MNI305.asl.nii.gz/ output data didn't work for right
> > hemisphere :
> >
> > /mri_surf2vol --surfval lh.fsaverage.asl --fillribbon --identity
> > fsaverage --template fsaverage/mri/T1.mgz --hemi lh --o
> > lh.MNI305.asl.nii.gz
> >
> > mri_surf2vol --surfval rh.fsaverage.asl --fillribbon --identity
> > fsaverage --merge lh.MNI305.asl.nii.gz --hemi rh --o MNI305.asl.nii.gz/
> >
> > What should I have to do ?
> >
> > Many thanks in advance for helping !
> >
> > Best regards,
> >
> > Matthieu
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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>
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Re: [Freesurfer] [FreeSurfer] : Convert asl data from fsaverage (surface) to MNI305 (volume)

[Matthieu Vanhoutte]

Hello Douglas,

I have downloaded a new license and it successfully runs !

Best regards,

Matthieu

2015-03-31 12:39 GMT+02:00 Matthieu Vanhoutte :

> Hello Douglas,
>
> I have download the new version of mri_surf2vol you supplied me, and have
> copied it in the FS5.3 /bin installation files.
>
> But when I tried to launch with my precedent command lines, the error
> message appeared :
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *gdiagno = -1Using identity matrix for
> registration--GNU
> libc version: 2.19ERROR: Systems running GNU glibc version greater than
> 2.15  require a newly formatted license file (it's free). Please  download
> a new one from the following page:
> http://surfer.nmr.mgh.harvard.edu/registration.html
> <http://surfer.nmr.mgh.harvard.edu/registration.html>--gdiagno
> = -1Using merge volume as templateUsing identity matrix for
> registrationniiRead(): error opening file
> /home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI305.asl.nii.gzmri_surf2vol
> ERROR: reading
> /home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI305.asl.nii.gz
> headerMatrix from regfile: 0.998  -0.007   0.018   0.957;-0.013  -0.009
> 0.997  -17.816;-0.015  -1.001   0.002  -18.550; 0.000   0.000   0.000
> 1.000;movvol /home/global//fsl50/data/standard/MNI152_T1_2mm.nii.gztargvol
> /home/fatmike/sebastien/FS5.1/207020_T0/asl/MNI305.asl.nii.gzoutvol
> /home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI152.asl.nii.gzregfile
> /home/global//freesurfer5.3//average/mni152.register.datinvert 1tal
> 0talres 2regheader 0noresample 0interp  nearest (0)precision  float
> (3)Gdiag_no  -1Synth  0SynthSeed  1427897150Invert!niiRead(): error
> opening file /home/fatmike/sebastien/FS5.1/207020_T0/asl/MNI305.asl.nii.gz*
>
> What shoul I do ?
>
> Best regards,
>
> Matthieu
>
>
> 2015-03-26 21:27 GMT+01:00 Douglas N Greve :
>
>>
>> That version had a bug. Try this version
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
>>
>> On 03/26/2015 12:16 PM, Matthieu Vanhoutte wrote:
>> > Dear experts,
>> >
>> > I have some asl data on fsaverage surface and would like to compute
>> > them on MNI305 volume. So I executed the commands below, but when
>> > merging left and right hemispheres it seems that the /--fillribbon
>> > /option on /MNI305.asl.nii.gz/ output data didn't work for right
>> > hemisphere :
>> >
>> > /mri_surf2vol --surfval lh.fsaverage.asl --fillribbon --identity
>> > fsaverage --template fsaverage/mri/T1.mgz --hemi lh --o
>> > lh.MNI305.asl.nii.gz
>> >
>> > mri_surf2vol --surfval rh.fsaverage.asl --fillribbon --identity
>> > fsaverage --merge lh.MNI305.asl.nii.gz --hemi rh --o MNI305.asl.nii.gz/
>> >
>> > What should I have to do ?
>> >
>> > Many thanks in advance for helping !
>> >
>> > Best regards,
>> >
>> > Matthieu
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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[Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

[Matthieu Vanhoutte]

Dear experts,

I had to make volumic statistical analysis for the need to use BPM toolbox.
So, I got in the output of this statistical analysis some volumic Tmaps.

As I did before some group analysis according to FStutorial, I would like
to apply the same method of Clusterwise Correction on my volumic Tmaps. I
have projected my Tmpas on fsaverage surface, but don't know if it is
possible to apply multiple comparisons correction on these ? And if it is
the case, how to do it ?

Thanks in advance for any help you could supply to me !

Best regards,

Matthieu
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Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

[Matthieu Vanhoutte]

Hello Douglas,

Thanks but even if I do the clusterwise correction in the volume, I can't
get an clusterwise corrected output volume image. The only things I have
are the Tmaps that I can threshold if wanted.

And I would like to project on fsaverage surface the results of the
clusterwise correction in the volume. How could I do ?

Best regards,

Matthieu

2015-04-13 16:27 GMT+02:00 Douglas Greve :

>  If you did the analysis in the volume, then you have to do the
> clusterwise correction in the volume.
>
>
> On 4/13/15 6:05 AM, Matthieu Vanhoutte wrote:
>
>  Dear experts,
>
>  I had to make volumic statistical analysis for the need to use BPM
> toolbox. So, I got in the output of this statistical analysis some volumic
> Tmaps.
>
>  As I did before some group analysis according to FStutorial, I would
> like to apply the same method of Clusterwise Correction on my volumic
> Tmaps. I have projected my Tmpas on fsaverage surface, but don't know if it
> is possible to apply multiple comparisons correction on these ? And if it
> is the case, how to do it ?
>
>  Thanks in advance for any help you could supply to me !
>
>  Best regards,
>
>  Matthieu
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

[Matthieu Vanhoutte]

By the mean of SPM, the Biological Parmatring toolbox can do the FWE
correction and give me results on a glass brain. But I don't have any
cluster wise corrected P-maps on output.

Or did I miss something ?

Best regards,

Matthieu

2015-04-13 16:51 GMT+02:00 Douglas Greve :

>  Does the BPM toolbox (what's that?) not give you cluster correction? You
> can try using mri_volcluster with the --grf option, but you'll need to know
> the FWHM. Afterwards you can map the result to the surface
>
>
> On 4/13/15 10:46 AM, Matthieu Vanhoutte wrote:
>
>  Hello Douglas,
>
>  Thanks but even if I do the clusterwise correction in the volume, I can't
> get an clusterwise corrected output volume image. The only things I have
> are the Tmaps that I can threshold if wanted.
>
>  And I would like to project on fsaverage surface the results of the
> clusterwise correction in the volume. How could I do ?
>
>  Best regards,
>
>  Matthieu
>
> 2015-04-13 16:27 GMT+02:00 Douglas Greve :
>
>>  If you did the analysis in the volume, then you have to do the
>> clusterwise correction in the volume.
>>
>>
>> On 4/13/15 6:05 AM, Matthieu Vanhoutte wrote:
>>
>>   Dear experts,
>>
>>  I had to make volumic statistical analysis for the need to use BPM
>> toolbox. So, I got in the output of this statistical analysis some volumic
>> Tmaps.
>>
>>  As I did before some group analysis according to FStutorial, I would
>> like to apply the same method of Clusterwise Correction on my volumic
>> Tmaps. I have projected my Tmpas on fsaverage surface, but don't know if it
>> is possible to apply multiple comparisons correction on these ? And if it
>> is the case, how to do it ?
>>
>>  Thanks in advance for any help you could supply to me !
>>
>>  Best regards,
>>
>>  Matthieu
>>
>>
>>  ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> ___
> Freesurfer mailing 
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

[Matthieu Vanhoutte]

Thank you Douglas !

Matthieu

2015-04-13 22:13 GMT+02:00 Douglas N Greve :

> clusterwise correction is a type of FWE correction. If the FWE you are
> using is good enough for you and you want to visualize the results on a
> surface, then use mri_vol2surf. If this was done on the SPM template
> space, then run the SPM T1 template through recon-all to get the surfaces
>
>
>
>
>
>
> On 04/13/2015 11:09 AM, Matthieu Vanhoutte wrote:
> > By the mean of SPM, the Biological Parmatring toolbox can do the FWE
> > correction and give me results on a glass brain. But I don't have any
> > cluster wise corrected P-maps on output.
> >
> > Or did I miss something ?
> >
> > Best regards,
> >
> > Matthieu
> >
> > 2015-04-13 16:51 GMT+02:00 Douglas Greve  > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> > Does the BPM toolbox (what's that?) not give you cluster
> > correction? You can try using mri_volcluster with the --grf
> > option, but you'll need to know the FWHM. Afterwards you can map
> > the result to the surface
> >
> >
> > On 4/13/15 10:46 AM, Matthieu Vanhoutte wrote:
> >> Hello Douglas,
> >>
> >> Thanks but even if I do the clusterwise correction in the volume,
> >> I can't get an clusterwise corrected output volume image. The
> >> only things I have are the Tmaps that I can threshold if wanted.
> >>
> >> And I would like to project on fsaverage surface the results of
> >> the clusterwise correction in the volume. How could I do ?
> >>
> >> Best regards,
> >>
> >>     Matthieu
> >>
> >> 2015-04-13 16:27 GMT+02:00 Douglas Greve
> >> mailto:gr...@nmr.mgh.harvard.edu>>:
> >>
> >> If you did the analysis in the volume, then you have to do
> >> the clusterwise correction in the volume.
> >>
> >>
> >> On 4/13/15 6:05 AM, Matthieu Vanhoutte wrote:
> >>> Dear experts,
> >>>
> >>> I had to make volumic statistical analysis for the need to
> >>> use BPM toolbox. So, I got in the output of this statistical
> >>> analysis some volumic Tmaps.
> >>>
> >>> As I did before some group analysis according to FStutorial,
> >>> I would like to apply the same method of Clusterwise
> >>> Correction on my volumic Tmaps. I have projected my Tmpas on
> >>> fsaverage surface, but don't know if it is possible to apply
> >>> multiple comparisons correction on these ? And if it is the
> >>> case, how to do it ?
> >>>
> >>> Thanks in advance for any help you could supply to me !
> >>>
> >>> Best regards,
> >>>
> >>> Matthieu
> >>>
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu   Freesurfer@nmr.mgh.harvard.edu>
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> The information in this e-mail is intended only for the
> >> person to whom it is
> >> addressed. If you believe this e-mail was sent to you in
> >> error and the e-mail
> >> contains patient information, please contact the Partners
> >> Compliance HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was
> >> sent to you in error
> >> but does not contain patient information, please contact the
> >> sender and properly
> >> dispose of the e-mail.
> >>
> >>
> >>
> >>
> >> ___
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> >
> >
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[Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

[Matthieu Vanhoutte]

Dear FreeSurfer's experts,

For personnal need I use the BPM toolbox (Biological Parametric Mapping) to
compute GLM analysis. The outputs of this Toolbox gave me beta maps and
Tmaps.

However, precedently I used the whole FreeSurfer group analysis tutorial on
other datas, including the Clusterwise Correction for multiple comparisons.
And now in order to compare results, I'd like to use this Clusterwise
Correction consequently to my BPM Toolbox GLM analysis.

Is it possible to manually adapt some scripts ? In this way, how could I
upgrade my outputs to these of "mri_glmfit" in order to launch Clusterwise
Correction after ?

Many thanks in advance for helping !

Best regards,

Matthieu
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Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

[Matthieu Vanhoutte]

Hello Douglas,

Indeed BPM doesn't do Clusterwise correction.

What does the FWHM of the BPM analysis correspond to ? And how to find it ?

Manu thanks !

Best regards,

Matthieu
Le 15 avr. 2015 00:23, "Douglas Greve"  a écrit :

>  So BPM does not do clusterwise correction? You could use mri_volcluster,
> but you'll need to know the FWHM of your BPM analysis
> doug
>
> On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote:
>
>   Dear FreeSurfer's experts,
>
>  For personnal need I use the BPM toolbox (Biological Parametric Mapping)
> to compute GLM analysis. The outputs of this Toolbox gave me beta maps and
> Tmaps.
>
> However, precedently I used the whole FreeSurfer group analysis tutorial
> on other datas, including the Clusterwise Correction for multiple
> comparisons. And now in order to compare results, I'd like to use this
> Clusterwise Correction consequently to my BPM Toolbox GLM analysis.
>
>  Is it possible to manually adapt some scripts ? In this way, how could I
> upgrade my outputs to these of "mri_glmfit" in order to launch Clusterwise
> Correction after ?
>
>  Many thanks in advance for helping !
>
>  Best regards,
>
>   Matthieu
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

[Matthieu Vanhoutte]

Hello Douglas,

Sorry if I haven't been clear. I'm trying to explain my needs :

1) I use the BPM toolbox to compute the GLM analysis as mri_glmfit would
do. However, outputs of this toolbox only give me beta maps and uncorrected
Tmaps.
2) With only these uncorrected Tmaps outputs, I'd like to apply Clusterwise
correction as mri_glmfit-sim would do with the same arguments if possible
(--cache ; --cwp ; --2spaces ; ...).

--> Is there a way to succeed in 2) with some manual scripting ?

--> Is the mri_volcluster adapted as you proposed : in this case you said I
need to know the FWHM of my BPM analysis, how could I obtain this ?

--> Would I have access in this way to arguments --cache and --cwp as used
in mri_glmfit-sim ?

I hope I have been clearly.

Thanks in advance for guiding me !

Best regards,

Matthieu

2015-04-15 3:06 GMT+02:00 Douglas Greve :

>  I guess I don't understand what you are asking for. If BPM outputs a
> cluster-corrected volume, then why can't you just map that to the surface
> and be done with it?
>
>
> On 4/14/15 6:48 PM, Matthieu Vanhoutte wrote:
>
> Hello Douglas,
>
> Indeed BPM doesn't do Clusterwise correction.
>
> What does the FWHM of the BPM analysis correspond to ? And how to find it ?
>
> Manu thanks !
>
> Best regards,
>
> Matthieu
> Le 15 avr. 2015 00:23, "Douglas Greve"  a
> écrit :
>
>>  So BPM does not do clusterwise correction? You could use mri_volcluster,
>> but you'll need to know the FWHM of your BPM analysis
>> doug
>>
>> On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote:
>>
>>   Dear FreeSurfer's experts,
>>
>>  For personnal need I use the BPM toolbox (Biological Parametric Mapping)
>> to compute GLM analysis. The outputs of this Toolbox gave me beta maps and
>> Tmaps.
>>
>> However, precedently I used the whole FreeSurfer group analysis tutorial
>> on other datas, including the Clusterwise Correction for multiple
>> comparisons. And now in order to compare results, I'd like to use this
>> Clusterwise Correction consequently to my BPM Toolbox GLM analysis.
>>
>>  Is it possible to manually adapt some scripts ? In this way, how could I
>> upgrade my outputs to these of "mri_glmfit" in order to launch Clusterwise
>> Correction after ?
>>
>>  Many thanks in advance for helping !
>>
>>  Best regards,
>>
>>   Matthieu
>>
>>
>> ___
>> Freesurfer mailing 
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>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> dispose of the e-mail.
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Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

[Matthieu Vanhoutte]

Thank you Douglas for this detailed answer.

Matthieu

2015-04-15 15:19 GMT+02:00 Douglas Greve :

>  Sorry, I misread your previous email as "Indeed BPM does do Clusterwise
> correction." instead of "Indeed BPM doesn't do Clusterwise correction." The
> FWHM is the full-width-half-max and is a measure of the spatial smoothness.
> This is always needed for cluster-wise correction. This is usually obtained
> during the group analysis by examining the residuals, so it should come out
> of what  ever you are using for group analysis. If it does not come out of
> BPM, then that is a problem that I cannot help you with (talk to whoever
> programmed BPM).
>
> doug
>
>
> On 4/15/15 3:30 AM, Matthieu Vanhoutte wrote:
>
>  Hello Douglas,
>
>  Sorry if I haven't been clear. I'm trying to explain my needs :
>
>  1) I use the BPM toolbox to compute the GLM analysis as mri_glmfit would
> do. However, outputs of this toolbox only give me beta maps and uncorrected
> Tmaps.
>  2) With only these uncorrected Tmaps outputs, I'd like to apply
> Clusterwise correction as mri_glmfit-sim would do with the same arguments
> if possible (--cache ; --cwp ; --2spaces ; ...).
>
>  --> Is there a way to succeed in 2) with some manual scripting ?
>
> --> Is the mri_volcluster adapted as you proposed : in this case you said
> I need to know the FWHM of my BPM analysis, how could I obtain this ?
>
>  --> Would I have access in this way to arguments --cache and --cwp as
> used in mri_glmfit-sim ?
>
>  I hope I have been clearly.
>
>  Thanks in advance for guiding me !
>
>  Best regards,
>
>  Matthieu
>
> 2015-04-15 3:06 GMT+02:00 Douglas Greve :
>
>>  I guess I don't understand what you are asking for. If BPM outputs a
>> cluster-corrected volume, then why can't you just map that to the surface
>> and be done with it?
>>
>>
>> On 4/14/15 6:48 PM, Matthieu Vanhoutte wrote:
>>
>> Hello Douglas,
>>
>> Indeed BPM doesn't do Clusterwise correction.
>>
>> What does the FWHM of the BPM analysis correspond to ? And how to find it
>> ?
>>
>> Manu thanks !
>>
>> Best regards,
>>
>> Matthieu
>> Le 15 avr. 2015 00:23, "Douglas Greve"  a
>> écrit :
>>
>>>  So BPM does not do clusterwise correction? You could use
>>> mri_volcluster, but you'll need to know the FWHM of your BPM analysis
>>> doug
>>>
>>> On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote:
>>>
>>>   Dear FreeSurfer's experts,
>>>
>>>  For personnal need I use the BPM toolbox (Biological Parametric
>>> Mapping) to compute GLM analysis. The outputs of this Toolbox gave me beta
>>> maps and Tmaps.
>>>
>>> However, precedently I used the whole FreeSurfer group analysis tutorial
>>> on other datas, including the Clusterwise Correction for multiple
>>> comparisons. And now in order to compare results, I'd like to use this
>>> Clusterwise Correction consequently to my BPM Toolbox GLM analysis.
>>>
>>>  Is it possible to manually adapt some scripts ? In this way, how could
>>> I upgrade my outputs to these of "mri_glmfit" in order to launch
>>> Clusterwise Correction after ?
>>>
>>>  Many thanks in advance for helping !
>>>
>>>  Best regards,
>>>
>>>   Matthieu
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>> ___
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>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.h

[Freesurfer] Compute residual FWHM in GLM group analyses

[Matthieu Vanhoutte]

Dear experts,

I have run GLM group analyses on another software than FreeSurfer for
personal needs. I have now beta coefficients and residual datas on
fsaverage space.

I'd like to use then the clusterwise correction for multiple comparisons
provided by FreeSurfer. But I need for that to know the residual FWHM.

How could I compute it with residual datas on fsaverage space ?

Many thanks in advance !

Best regards,

Matthieu
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Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

[Matthieu Vanhoutte]

Dear experts,

I would like to use the clusterwise correction specified in the group
analysis FreeSurfer wiki (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). In
this way, I would use mri_surfcluster with the known FWHM of my GLM
analysis and my input is an *uncorrected Tmap*. However, in the group
analysis wiki, the input for the mri_surfcluster command is :

*sig.mgh -- significance, -log10(pvalue), uncorrected (surface overlay)*

So, could I use my uncorrected Tmap instead of sig.mgh or should I
apply a transform to obtain kinf of -log10(pvalue) ? Is this is the
case how to convert Tmap ?

Many thanks in advance for helping !

Best regards,

Matthieu

2015-04-15 15:19 GMT+02:00 Douglas Greve :

>  Sorry, I misread your previous email as "Indeed BPM does do Clusterwise
> correction." instead of "Indeed BPM doesn't do Clusterwise correction." The
> FWHM is the full-width-half-max and is a measure of the spatial smoothness.
> This is always needed for cluster-wise correction. This is usually obtained
> during the group analysis by examining the residuals, so it should come out
> of what  ever you are using for group analysis. If it does not come out of
> BPM, then that is a problem that I cannot help you with (talk to whoever
> programmed BPM).
>
> doug
>
>
> On 4/15/15 3:30 AM, Matthieu Vanhoutte wrote:
>
>  Hello Douglas,
>
>  Sorry if I haven't been clear. I'm trying to explain my needs :
>
>  1) I use the BPM toolbox to compute the GLM analysis as mri_glmfit would
> do. However, outputs of this toolbox only give me beta maps and uncorrected
> Tmaps.
>  2) With only these uncorrected Tmaps outputs, I'd like to apply
> Clusterwise correction as mri_glmfit-sim would do with the same arguments
> if possible (--cache ; --cwp ; --2spaces ; ...).
>
>  --> Is there a way to succeed in 2) with some manual scripting ?
>
> --> Is the mri_volcluster adapted as you proposed : in this case you said
> I need to know the FWHM of my BPM analysis, how could I obtain this ?
>
>  --> Would I have access in this way to arguments --cache and --cwp as
> used in mri_glmfit-sim ?
>
>  I hope I have been clearly.
>
>  Thanks in advance for guiding me !
>
>  Best regards,
>
>  Matthieu
>
> 2015-04-15 3:06 GMT+02:00 Douglas Greve :
>
>>  I guess I don't understand what you are asking for. If BPM outputs a
>> cluster-corrected volume, then why can't you just map that to the surface
>> and be done with it?
>>
>>
>> On 4/14/15 6:48 PM, Matthieu Vanhoutte wrote:
>>
>> Hello Douglas,
>>
>> Indeed BPM doesn't do Clusterwise correction.
>>
>> What does the FWHM of the BPM analysis correspond to ? And how to find it
>> ?
>>
>> Manu thanks !
>>
>> Best regards,
>>
>> Matthieu
>> Le 15 avr. 2015 00:23, "Douglas Greve"  a
>> écrit :
>>
>>>  So BPM does not do clusterwise correction? You could use
>>> mri_volcluster, but you'll need to know the FWHM of your BPM analysis
>>> doug
>>>
>>> On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote:
>>>
>>>   Dear FreeSurfer's experts,
>>>
>>>  For personnal need I use the BPM toolbox (Biological Parametric
>>> Mapping) to compute GLM analysis. The outputs of this Toolbox gave me beta
>>> maps and Tmaps.
>>>
>>> However, precedently I used the whole FreeSurfer group analysis tutorial
>>> on other datas, including the Clusterwise Correction for multiple
>>> comparisons. And now in order to compare results, I'd like to use this
>>> Clusterwise Correction consequently to my BPM Toolbox GLM analysis.
>>>
>>>  Is it possible to manually adapt some scripts ? In this way, how could
>>> I upgrade my outputs to these of "mri_glmfit" in order to launch
>>> Clusterwise Correction after ?
>>>
>>>  Many thanks in advance for helping !
>>>
>>>  Best regards,
>>>
>>>   Matthieu
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you belie

Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

[Matthieu Vanhoutte]

Hello Douglas,

What do you mean by not doing the adjustement for 1-tailed test ? Does this
mean specify the sign as "abs" ?

I don't understand well how -log10(p) could be negative with 0 a écrit :

>  I think it should work with a t as input. When you set the threshold, put
> in the t-value you want, not a -log10(p). Also, don't do the adjustment for
> 1-tailed test because then it will interpret the input as -log10(p).
>
> On 5/29/15 10:46 AM, Matthieu Vanhoutte wrote:
>
>  Dear experts,
>
>  I would like to use the clusterwise correction specified in the group
> analysis FreeSurfer wiki (
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). In
> this way, I would use mri_surfcluster with the known FWHM of my GLM
> analysis and my input is an *uncorrected Tmap*. However, in the group
> analysis wiki, the input for the mri_surfcluster command is :
>
> *sig.mgh -- significance, -log10(pvalue), uncorrected (surface overlay)*
>
> So, could I use my uncorrected Tmap instead of sig.mgh or should I apply a 
> transform to obtain kinf of -log10(pvalue) ? Is this is the case how to 
> convert Tmap ?
>
> Many thanks in advance for helping !
>
> Best regards,
>
> Matthieu
>
>  2015-04-15 15:19 GMT+02:00 Douglas Greve :
>
>>  Sorry, I misread your previous email as "Indeed BPM does do Clusterwise
>> correction." instead of "Indeed BPM doesn't do Clusterwise correction." The
>> FWHM is the full-width-half-max and is a measure of the spatial smoothness.
>> This is always needed for cluster-wise correction. This is usually obtained
>> during the group analysis by examining the residuals, so it should come out
>> of what  ever you are using for group analysis. If it does not come out of
>> BPM, then that is a problem that I cannot help you with (talk to whoever
>> programmed BPM).
>>
>> doug
>>
>>
>> On 4/15/15 3:30 AM, Matthieu Vanhoutte wrote:
>>
>>  Hello Douglas,
>>
>>  Sorry if I haven't been clear. I'm trying to explain my needs :
>>
>>  1) I use the BPM toolbox to compute the GLM analysis as mri_glmfit would
>> do. However, outputs of this toolbox only give me beta maps and uncorrected
>> Tmaps.
>>  2) With only these uncorrected Tmaps outputs, I'd like to apply
>> Clusterwise correction as mri_glmfit-sim would do with the same arguments
>> if possible (--cache ; --cwp ; --2spaces ; ...).
>>
>>  --> Is there a way to succeed in 2) with some manual scripting ?
>>
>> --> Is the mri_volcluster adapted as you proposed : in this case you said
>> I need to know the FWHM of my BPM analysis, how could I obtain this ?
>>
>>  --> Would I have access in this way to arguments --cache and --cwp as
>> used in mri_glmfit-sim ?
>>
>>  I hope I have been clearly.
>>
>>  Thanks in advance for guiding me !
>>
>>  Best regards,
>>
>>  Matthieu
>>
>> 2015-04-15 3:06 GMT+02:00 Douglas Greve :
>>
>>>  I guess I don't understand what you are asking for. If BPM outputs a
>>> cluster-corrected volume, then why can't you just map that to the surface
>>> and be done with it?
>>>
>>>
>>> On 4/14/15 6:48 PM, Matthieu Vanhoutte wrote:
>>>
>>> Hello Douglas,
>>>
>>> Indeed BPM doesn't do Clusterwise correction.
>>>
>>> What does the FWHM of the BPM analysis correspond to ? And how to find
>>> it ?
>>>
>>> Manu thanks !
>>>
>>> Best regards,
>>>
>>> Matthieu
>>> Le 15 avr. 2015 00:23, "Douglas Greve"  a
>>> écrit :
>>>
>>>>  So BPM does not do clusterwise correction? You could use
>>>> mri_volcluster, but you'll need to know the FWHM of your BPM analysis
>>>> doug
>>>>
>>>> On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote:
>>>>
>>>>   Dear FreeSurfer's experts,
>>>>
>>>>  For personnal need I use the BPM toolbox (Biological Parametric
>>>> Mapping) to compute GLM analysis. The outputs of this Toolbox gave me beta
>>>> maps and Tmaps.
>>>>
>>>> However, precedently I used the whole FreeSurfer group analysis
>>>> tutorial on other datas, including the Clusterwise Correction for multiple
>>>> comparisons. And now in order to compare results, I'd like to use this
>>>> Clusterwise Correction consequently to my BPM Toolbox GLM analysis.
>>>>
>>>>  Is it possible to manually a

Re: [Freesurfer] GLM analysis on CBF maps

[Matthieu Vanhoutte]

Dear Experts,

I have run GLM group analyses with Freesurfer tools according DODS 
model, with six classes ((Male,Female) ; (Control,Left,Right)) and one 
age variable :


/Class MaleControl
Class MaleLeft
Class MaleRight
Class FemaleControl
Class FemaleLeft
Class FemaleRight
Variables Age

/However, I would like to consider gender as covariable of my GLM 
design. So, should I as done consider gender as discret factor and part 
of CLASS/group or should I consider gender as a continuous variable (0 = 
male, 1 =  female) and add a column on the Variables line of the FSGD 
file near Age (/Variables Age Gender) ?


/Many thanks in advance for helping !

Best regards,
Matthieu/
/

On 3/12/15 1:30 PM, Matthieu Vanhoutte wrote:

Hello,

I have run GLM group analyses with Freesurfer tools according DODS 
model, with six classes ((Male,Female) ; (Control,Left,Right)) and 
one age variable :


/Class MaleControl
Class MaleLeft
Class MaleRight
Class FemaleControl
Class FemaleLeft
Class FemaleRight
Variables Age /

I wanted to test /Control > Left/ and /Control > Right/ on CBF maps. 
I defined with help of the tutorial contrats for that :


/control-left.intercept.mtx : 0.5 -0.5 0 0.5 -0.5 0 0 0 0 0 0 0
control-left.slope.mtx : 0 0 0 0 0 0 0.5 -0.5 0 0.5 -0.5 0
control-right.intercept.mtx : 0.5 0 -0.5 0.5 0 -0.5 0 0 0 0 0 0
control-right.slope.mtx : 0 0 0 0 0 0 0.5 0 -0.5 0.5 0 -0.5/

My problem is that I don't know how to interpret significative 
results in both /Control > Left /contrasts/: 
//control-left.intercept.mtx /and///control-left.slope.mtx. /The same 
for/Control > Right./ One is coding for intercept and the other for 
slope, but concretely what significative results in both contrasts mean ?


Thank you in advance for helping !

Best regards,

-----
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-03-11 16:51 GMT+01:00 Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>>:



the sig value is actually  -log10(p)*sign(gamma) where gamma
is the
contrast (gamma.mgh). The p-value is two-tailed, and the color
indicates
what tail you are on.
doug

    On 03/10/2015 01:21 PM, Matthieu Vanhoutte wrote:
> Dear FreeSurfer's experts,
>
> I have launched a GLM analyses following the tutorial :
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>
> Below the command I have used :
>
> /mri_glmfit \
>   --y
>

${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.all.subjects.fwhm3.fsaverage.cbf_s.mgh
> \
>   --fsgd ${FS_DIR}/SurfaceAnalysis_mri_glmfit/g6v1.fsgd dods \
>   --C
${FS_DIR}/SurfaceAnalysis_mri_glmfit/control-left.intercept.mtx \
>   --surf fsaverage lh \
>   --cortex \
>   --glmdir ${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/
>
>
> In order to see the uncorrected results with p<.0001, I ran :
>
> /freeview -f
> 
${SUBJECTS_DIR}/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=${SUBJECTS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/control-left.intercept/sig.mgh:overlay_threshold=4,5
> -viewport 3d/
>
> However, nothing appears with this threshold and when I wanted to
> configure overlay I saw that most of my values in /sig.mgh /were
> negatives between -4 and 0...
>
> How is possible for /-log10(pvalue)/ values ? Could I obtain
> significant uncorrected values from this /sig.mgh/ file ?
>
> Please find attached my needed files : *y.fsgd, mri_glmfit.log,
> **/control-left.intercept.mtx/ and sig.mgh *
>
> Thank you in advance for helping me !!
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
>
> ___
> Freesurfer mailing list
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 
Fax: 617-726-7422 

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[Freesurfer] [FreeSurfer] Multiple overlays on surface

[Matthieu Vanhoutte]

Dear FreeSurfer's experts,

I would like to visualize on freeview two overlays on fsaverage cortical
surface.

I have used the code below found on the mailing list :




*mri_binarize --i sig1.mgh --min 0.1 --binval 1 --o sig1_th.mghmri_binarize
--i sig2.mgh --min 0.1 --binval 2 --o sig2_th.mgh*


*fscalc sig1_th.mgh add sig2_th.mgh --o sig1_sig2.mghmris_seg2annot --seg
sig1_sig2.mgh --ctab sig1_sig2_LUT.txt --s fsaverage --h lh --o
sig1_sig2.annot*

with sig1_sig2.annot defined as below :

#No. Label Name:R   G   B   A

0   Unknown 128   128   128   0
1   sig1 70  130 180 0
2   sig2 245 245 245 0
3   Overlay_sig1_sig2 205 62  78  0

My problem is that I'd like to view my cortical suface with binary
curvature where there is no value (=0). Could I specify the unknown label
(0) to be transparent or anything that could solve the mater ?

Best regards,

Matthieu
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Re: [Freesurfer] [FreeSurfer] Multiple overlays on surface

[Matthieu Vanhoutte]

I tried it but gave me a black surface.
Le 6 juin 2015 00:06, "Douglas N Greve"  a
écrit :

> Try it with 0 0 0 instead of 128 128 128
>
> On 06/05/2015 07:44 AM, Matthieu Vanhoutte wrote:
> > Dear FreeSurfer's experts,
> >
> > I would like to visualize on freeview two overlays on fsaverage
> > cortical surface.
> >
> > I have used the code below found on the mailing list :
> >
> > /mri_binarize --i sig1.mgh --min 0.1 --binval 1 --o sig1_th.mgh
> > mri_binarize --i sig2.mgh --min 0.1 --binval 2 --o sig2_th.mgh
> >
> > /
> > /fscalc sig1_th.mgh add sig2_th.mgh --o sig1_sig2.mgh
> >
> > mris_seg2annot --seg sig1_sig2.mgh --ctab sig1_sig2_LUT.txt --s
> > fsaverage --h lh --o sig1_sig2.annot/
> >
> > with sig1_sig2.annot defined as below :
> >
> > #No. Label Name:R   G B   A
> >
> > 0   Unknown 128 128   128   0
> > 1   sig1 70 130 180 0
> > 2   sig2 245 245 245 0
> > 3   Overlay_sig1_sig2 205 62 78  0
> >
> > My problem is that I'd like to view my cortical suface with binary
> > curvature where there is no value (=0). Could I specify the unknown
> > label (0) to be transparent or anything that could solve the mater ?
> >
> > Best regards,
> >
> > Matthieu
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] [FreeSurfer] Multiple overlays on surface

[Matthieu Vanhoutte]

Hi Douglas,

you can find below the command on input and the terminal output for
mris_seg2annot :


















*mris_seg2annot --seg ./cache.th13.pos.sig.cluster_cbf_ct.mgh --ctab
./Overlay_CBF_CT_CSvsL_LUT.txt --s fsaverage --h lh --o
./lh.CBF_CT.annot$Id: mris_seg2annot.c,v 1.9 2011/03/02 00:04:34 nicks Exp
$cwd
/NAS/dumbo/matthieu/ASL_Epilepsy/FS_5.3/SurfaceAnalysis_mri_glmfit/V1/DODScmdline
mris_seg2annot --seg ./cache.th13.pos.sig.cluster_cbf_ct.mgh --ctab
./Overlay_CBF_CT_CSvsL_LUT.txt --s fsaverage --h lh --o ./lh.CBF_CT.annot
sysname  Linuxhostname yakuzamachine  x86_64user matthieusubject
fsaveragehemi  lhsurfseg
./cache.th13.pos.sig.cluster_cbf_ct.mghctab
./Overlay_CBF_CT_CSvsL_LUT.txtannotfile ./lh.CBF_CT.annotReading ctab
./Overlay_CBF_CT_CSvsL_LUT.txtReading surface seg
./cache.th13.pos.sig.cluster_cbf_ct.mghReading surface
/NAS/dumbo/matthieu/ASL_Epilepsy/FS_5.3/fsaverage/surf/lh.whiteWriting
annot to ./lh.CBF_CT.annot*

Best regards,

Matthieu

2015-06-06 0:15 GMT+02:00 Douglas N Greve :

> what is the terminal output for mris_seg2annot?
>
> On 06/05/2015 06:12 PM, Matthieu Vanhoutte wrote:
> >
> > I tried it but gave me a black surface.
> >
> > Le 6 juin 2015 00:06, "Douglas N Greve"  > <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
> >
> > Try it with 0 0 0 instead of 128 128 128
> >
> > On 06/05/2015 07:44 AM, Matthieu Vanhoutte wrote:
> > > Dear FreeSurfer's experts,
> > >
> > > I would like to visualize on freeview two overlays on fsaverage
> > > cortical surface.
> > >
> > > I have used the code below found on the mailing list :
> > >
> > > /mri_binarize --i sig1.mgh --min 0.1 --binval 1 --o sig1_th.mgh
> > > mri_binarize --i sig2.mgh --min 0.1 --binval 2 --o sig2_th.mgh
> > >
> > > /
> > > /fscalc sig1_th.mgh add sig2_th.mgh --o sig1_sig2.mgh
> > >
> > > mris_seg2annot --seg sig1_sig2.mgh --ctab sig1_sig2_LUT.txt --s
> > > fsaverage --h lh --o sig1_sig2.annot/
> > >
> > > with sig1_sig2.annot defined as below :
> > >
> > > #No. Label Name:R   G B   A
> > >
> > > 0   Unknown 128 128  128   0
> > > 1   sig1 70 130 180 0
> > > 2   sig2 245 245 245 0
> > > 3   Overlay_sig1_sig2 205 62 78  0
> > >
> > > My problem is that I'd like to view my cortical suface with binary
> > > curvature where there is no value (=0). Could I specify the unknown
> > > label (0) to be transparent or anything that could solve the mater
> ?
> > >
> > > Best regards,
> > >
> > > Matthieu
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the
> > sender and properly
> 

[Freesurfer] Error while using "mri_glmfit"

[Matthieu Vanhoutte]

Dear Freesurfer's Experts,

Please find below an error occuring when I use mri_glmfit :

Design matrix --
 1.000   0.000   0.000   0.000   0.000   0.000   9.804   0.000   0.000
0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
-10.612   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
-21.114   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -12.936   0.000   0.000
0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   15.129
0.000   0.000   0.000   0.000   0.000   17.562   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   16.402   0.000   0.000
0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
-6.889   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   10.584   0.000
0.000   0.000   0.000   0.000   37.017   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   5.243
0.000   0.000   0.000   0.000   0.000   7.675   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   20.432
0.000   0.000   0.000   0.000   0.000   43.865   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   5.287   0.000
0.000   0.000   0.000   0.000   23.719   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   10.735   0.000   0.000
0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   3.734
0.000   0.000   0.000   0.000   0.000   21.167   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000  -8.197
0.000   0.000   0.000   0.000   0.000  -2.765   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -3.431   0.000   0.000
0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000
0.000   0.000  -18.456   0.000   0.000   0.000   0.000   0.000   4.976;
 1.000   0.000   0.000   0.000   0.000   0.000  -18.437   0.000   0.000
0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000   0.150   0.000   0.000   0.000   0.000   0.000  -1.417   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
-16.936   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000  -3.442   0.000
0.000   0.000   0.000   0.000   21.991   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   9.298   0.000   0.000
0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   6.360   0.000   0.000
0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -17.536   0.000   0.000   0.000   0.000   0.000   1.896   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -19.658   0.000   0.000   0.000   0.000   0.000  -5.226   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
1.919   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000   10.834   0.000   0.000   0.000   0.000   0.000   6.266   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -2.360   0.000   0.000
0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000  -1.939   0.000
0.000   0.000   0.000   0.000   17.494   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
-12.457   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000
0.000   0.000  -8.279   0.000   0.000   0.000   0.000   0.000   6.153;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
10.505   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
7.838   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000  -1.889   0.000
0.000   0.000   0.000   0.000  -12.457   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000
0.000   0.000   3.680   0.000   0.000   0.000   0.000   0.000  -8.888;
 0.

Re: [Freesurfer] Error while using "mri_glmfit"

[Matthieu Vanhoutte]

Hello experts,

Could anyone provide me an advice or answer to this problem ?

Thanks in advance !

Best regards,

Matthieu
Le 28 juil. 2015 14:12, "Matthieu Vanhoutte" 
a écrit :

> Dear Freesurfer's Experts,
>
> Please find below an error occuring when I use mri_glmfit :
>
> Design matrix --
>  1.000   0.000   0.000   0.000   0.000   0.000   9.804   0.000   0.000
> 0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
>  0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
> -10.612   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
>  0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
> -21.114   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
>  1.000   0.000   0.000   0.000   0.000   0.000  -12.936   0.000   0.000
> 0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
>  0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   15.129
> 0.000   0.000   0.000   0.000   0.000   17.562   0.000   0.000   0.000;
>  1.000   0.000   0.000   0.000   0.000   0.000   16.402   0.000   0.000
> 0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
>  0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
> -6.889   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
>  0.000   1.000   0.000   0.000   0.000   0.000   0.000   10.584   0.000
> 0.000   0.000   0.000   0.000   37.017   0.000   0.000   0.000   0.000;
>  0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   5.243
> 0.000   0.000   0.000   0.000   0.000   7.675   0.000   0.000   0.000;
>  0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   20.432
> 0.000   0.000   0.000   0.000   0.000   43.865   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000   0.000   0.000   0.000   5.287   0.000
> 0.000   0.000   0.000   0.000   23.719   0.000   0.000   0.000   0.000;
>  1.000   0.000   0.000   0.000   0.000   0.000   10.735   0.000   0.000
> 0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
>  0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   3.734
> 0.000   0.000   0.000   0.000   0.000   21.167   0.000   0.000   0.000;
>  0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000  -8.197
> 0.000   0.000   0.000   0.000   0.000  -2.765   0.000   0.000   0.000;
>  1.000   0.000   0.000   0.000   0.000   0.000  -3.431   0.000   0.000
> 0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
>  0.000   0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000
> 0.000   0.000  -18.456   0.000   0.000   0.000   0.000   0.000   4.976;
>  1.000   0.000   0.000   0.000   0.000   0.000  -18.437   0.000   0.000
> 0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
>  0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
> 0.000   0.150   0.000   0.000   0.000   0.000   0.000  -1.417   0.000;
>  0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
> -16.936   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
>  0.000   1.000   0.000   0.000   0.000   0.000   0.000  -3.442   0.000
> 0.000   0.000   0.000   0.000   21.991   0.000   0.000   0.000   0.000;
>  1.000   0.000   0.000   0.000   0.000   0.000   9.298   0.000   0.000
> 0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
>  1.000   0.000   0.000   0.000   0.000   0.000   6.360   0.000   0.000
> 0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
>  0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
> 0.000  -17.536   0.000   0.000   0.000   0.000   0.000   1.896   0.000;
>  0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
> 0.000  -19.658   0.000   0.000   0.000   0.000   0.000  -5.226   0.000;
>  0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
> 1.919   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
>  0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
> 0.000   10.834   0.000   0.000   0.000   0.000   0.000   6.266   0.000;
>  1.000   0.000   0.000   0.000   0.000   0.000  -2.360   0.000   0.000
> 0.000   0.000   0.000  -15.576   0.000   0.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000   0.000   0.000   0.000  -1.939   0.000
> 0.000   0.000   0.000   0.000   17.494   0.000   0.000   0.000   0.000;
>  0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000
> -12.457   0.000   0.000   0.000   0.000   0.000  -15.576   0.000   0.000;
>  0.000   0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000
> 0.000   0.000  -8.279   0.000   0.000   0.000   0.000   0.000   6.153;
>  0.000   0.000   0.000   1.000   0.000   0.00

Re: [Freesurfer] Error while using "mri_glmfit"

[Matthieu Vanhoutte]

Douglas,

Please fond attached the fsgd file.

Cheers,

Matthieu
Le 4 août 2015 21:45, "Douglas N Greve"  a
écrit :

> can you send the fsgd file?
>
> On 08/04/2015 03:42 PM, Matthieu Vanhoutte wrote:
> >
> > Hello experts,
> >
> > Could anyone provide me an advice or answer to this problem ?
> >
> > Thanks in advance !
> >
> > Best regards,
> >
> > Matthieu
> >
> > Le 28 juil. 2015 14:12, "Matthieu Vanhoutte"
> > mailto:matthieuvanhou...@gmail.com>> a
> > écrit :
> >
> > Dear Freesurfer's Experts,
> >
> > Please find below an error occuring when I use mri_glmfit :
> >
> > Design matrix --
> >  1.000   0.000   0.000   0.000   0.000   0.000 9.804   0.000
> > 0.000   0.000   0.000   0.000 -15.576   0.000   0.000   0.000
> > 0.000   0.000;
> >  0.000   0.000   0.000   1.000   0.000   0.000 0.000   0.000
> > 0.000  -10.612   0.000   0.000 0.000   0.000   0.000  -15.576
> > 0.000   0.000;
> >  0.000   0.000   0.000   1.000   0.000   0.000 0.000   0.000
> > 0.000  -21.114   0.000   0.000 0.000   0.000   0.000  -15.576
> > 0.000   0.000;
> >  1.000   0.000   0.000   0.000   0.000   0.000 -12.936   0.000
> > 0.000   0.000   0.000   0.000 -15.576   0.000   0.000   0.000
> > 0.000   0.000;
> >  0.000   0.000   1.000   0.000   0.000   0.000 0.000   0.000
> > 15.129   0.000   0.000   0.000 0.000   0.000   17.562   0.000
> > 0.000   0.000;
> >  1.000   0.000   0.000   0.000   0.000   0.000 16.402   0.000
> > 0.000   0.000   0.000   0.000 -15.576   0.000   0.000   0.000
> > 0.000   0.000;
> >  0.000   0.000   0.000   1.000   0.000   0.000 0.000   0.000
> > 0.000  -6.889   0.000   0.000 0.000   0.000   0.000  -15.576
> > 0.000   0.000;
> >  0.000   1.000   0.000   0.000   0.000   0.000 0.000   10.584
> > 0.000   0.000   0.000   0.000 0.000   37.017   0.000   0.000
> > 0.000   0.000;
> >  0.000   0.000   1.000   0.000   0.000   0.000 0.000   0.000
> > 5.243   0.000   0.000   0.000 0.000   0.000   7.675   0.000
> > 0.000   0.000;
> >  0.000   0.000   1.000   0.000   0.000   0.000 0.000   0.000
> > 20.432   0.000   0.000   0.000 0.000   0.000   43.865   0.000
> > 0.000   0.000;
> >  0.000   1.000   0.000   0.000   0.000   0.000 0.000   5.287
> > 0.000   0.000   0.000   0.000 0.000   23.719   0.000   0.000
> > 0.000   0.000;
> >  1.000   0.000   0.000   0.000   0.000   0.000 10.735   0.000
> > 0.000   0.000   0.000   0.000 -15.576   0.000   0.000   0.000
> > 0.000   0.000;
> >  0.000   0.000   1.000   0.000   0.000   0.000 0.000   0.000
> > 3.734   0.000   0.000   0.000 0.000   0.000   21.167   0.000
> > 0.000   0.000;
> >  0.000   0.000   1.000   0.000   0.000   0.000 0.000   0.000
> > -8.197   0.000   0.000   0.000 0.000   0.000  -2.765   0.000
> > 0.000   0.000;
> >  1.000   0.000   0.000   0.000   0.000   0.000 -3.431   0.000
> > 0.000   0.000   0.000   0.000 -15.576   0.000   0.000   0.000
> > 0.000   0.000;
> >  0.000   0.000   0.000   0.000   0.000   1.000 0.000   0.000
> > 0.000   0.000   0.000  -18.456 0.000   0.000   0.000   0.000
> > 0.000   4.976;
> >  1.000   0.000   0.000   0.000   0.000   0.000 -18.437   0.000
> > 0.000   0.000   0.000   0.000 -15.576   0.000   0.000   0.000
> > 0.000   0.000;
> >  0.000   0.000   0.000   0.000   1.000   0.000 0.000   0.000
> > 0.000   0.000   0.150   0.000 0.000   0.000   0.000   0.000
> > -1.417   0.000;
> >  0.000   0.000   0.000   1.000   0.000   0.000 0.000   0.000
> > 0.000  -16.936   0.000   0.000 0.000   0.000   0.000  -15.576
> > 0.000   0.000;
> >  0.000   1.000   0.000   0.000   0.000   0.000 0.000  -3.442
> > 0.000   0.000   0.000   0.000 0.000   21.991   0.000   0.000
> > 0.000   0.000;
> >  1.000   0.000   0.000   0.000   0.000   0.000 9.298   0.000
> > 0.000   0.000   0.000   0.000 -15.576   0.000   0.000   0.000
> > 0.000   0.000;
> >  1.000   0.000   0.000   0.000   0.000   0.000 6.360   0.000
> > 0.000   0.000   0.000   0.000 -15.576   0.000   0.000   0.000
> > 0.000   0.000;
> >  0.000   0.000   0.000   0.000   1.000   0.000 0.000   0.000
> > 0.000   0.000  -17.536   0.000 0.000   0.000   0.000   0.000
> > 1.896   0.000;
> >  0.000   0.000   0.000   0.000   1.000   0.000 0.000   0.

Re: [Freesurfer] Error while using "mri_glmfit"

[Matthieu Vanhoutte]

Thanks for quick answer ! How could I regress out the effect of epilepsy
duration on patients, knowing that this factor is null for controls ?

Cheers,

Matthieu
Le 4 août 2015 22:22, "Douglas N Greve"  a
écrit :

> The Epilepsy_Duration is the same for all MaleControl subjects. You
> can't use that as a covariate if it does not have any variation
>
> On 08/04/2015 04:10 PM, Matthieu Vanhoutte wrote:
> >
> > Douglas,
> >
> > Please fond attached the fsgd file.
> >
> > Cheers,
> >
> > Matthieu
> >
> > Le 4 août 2015 21:45, "Douglas N Greve"  > <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
> >
> > can you send the fsgd file?
> >
> > On 08/04/2015 03:42 PM, Matthieu Vanhoutte wrote:
> > >
> > > Hello experts,
> > >
> > > Could anyone provide me an advice or answer to this problem ?
> > >
> > > Thanks in advance !
> > >
> > > Best regards,
> > >
> > > Matthieu
> > >
> > > Le 28 juil. 2015 14:12, "Matthieu Vanhoutte"
> > >  > <mailto:matthieuvanhou...@gmail.com>
> > <mailto:matthieuvanhou...@gmail.com
> > <mailto:matthieuvanhou...@gmail.com>>> a
> > > écrit :
> > >
> > > Dear Freesurfer's Experts,
> > >
> > > Please find below an error occuring when I use mri_glmfit :
> > >
> > > Design matrix --
> > >  1.000   0.000   0.000   0.000   0.000   0.000 9.804  0.000
> > > 0.000   0.000   0.000   0.000 -15.576   0.000  0.000   0.000
> > > 0.000   0.000;
> > >  0.000   0.000   0.000   1.000   0.000   0.000 0.000  0.000
> > > 0.000  -10.612   0.000   0.000 0.000   0.000   0.000 -15.576
> > > 0.000   0.000;
> > >  0.000   0.000   0.000   1.000   0.000   0.000 0.000  0.000
> > > 0.000  -21.114   0.000   0.000 0.000   0.000   0.000 -15.576
> > > 0.000   0.000;
> > >  1.000   0.000   0.000   0.000   0.000   0.000 -12.936   0.000
> > > 0.000   0.000   0.000   0.000 -15.576   0.000  0.000   0.000
> > > 0.000   0.000;
> > >  0.000   0.000   1.000   0.000   0.000   0.000 0.000  0.000
> > > 15.129   0.000   0.000   0.000 0.000   0.000  17.562   0.000
> > > 0.000   0.000;
> > >  1.000   0.000   0.000   0.000   0.000   0.000 16.402   0.000
> > > 0.000   0.000   0.000   0.000 -15.576   0.000  0.000   0.000
> > > 0.000   0.000;
> > >  0.000   0.000   0.000   1.000   0.000   0.000 0.000  0.000
> > > 0.000  -6.889   0.000   0.000 0.000   0.000   0.000 -15.576
> > > 0.000   0.000;
> > >  0.000   1.000   0.000   0.000   0.000   0.000 0.000  10.584
> > > 0.000   0.000   0.000   0.000 0.000   37.017   0.000  0.000
> > > 0.000   0.000;
> > >  0.000   0.000   1.000   0.000   0.000   0.000 0.000  0.000
> > > 5.243   0.000   0.000   0.000 0.000   0.000   7.675  0.000
> > > 0.000   0.000;
> > >  0.000   0.000   1.000   0.000   0.000   0.000 0.000  0.000
> > > 20.432   0.000   0.000   0.000 0.000   0.000  43.865   0.000
> > > 0.000   0.000;
> > >  0.000   1.000   0.000   0.000   0.000   0.000 0.000  5.287
> > > 0.000   0.000   0.000   0.000 0.000   23.719   0.000  0.000
> > > 0.000   0.000;
> > >  1.000   0.000   0.000   0.000   0.000   0.000 10.735   0.000
> > > 0.000   0.000   0.000   0.000 -15.576   0.000  0.000   0.000
> > > 0.000   0.000;
> > >  0.000   0.000   1.000   0.000   0.000   0.000 0.000  0.000
> > > 3.734   0.000   0.000   0.000 0.000   0.000   21.167  0.000
> > > 0.000   0.000;
> > >  0.000   0.000   1.000   0.000   0.000   0.000 0.000  0.000
> > > -8.197   0.000   0.000   0.000 0.000   0.000  -2.765  0.000
> > > 0.000   0.000;
> > >  1.000   0.000   0.000   0.000   0.000   0.000 -3.431   0.000
> > > 0.000   0.000   0.000   0.000 -15.576   0.000  0.000   0.000
> > > 0.000   0.000;
> > >  0.000   0.000   0.000   0.000   0.000   1.000 0.000  0.000
> > > 0.000   0.000   0.000  -18.456 0.000   0.000   0.000  0.000
> > > 0.000   4.976;
> > 

[Freesurfer] Surface-based Cluster Summary Table as created by mri_glmfit-sim

[Matthieu Vanhoutte]

Hello Freesurfer's experts,

I used the group analysis clusterwise correction with glmfit-sim and I 
found that "Annot" field in Cluster Summary Table don't always fit well 
with the corresponding region on "?h.aparc.a2009s.annot" file.

How is determined precisely each localization of each cluster in the 
summary table ?

Thanks in advance !

Best regards,

Matthieu
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[Freesurfer] Surface-based Interhemispheric Registration : Compare left vs. right patients

[Matthieu Vanhoutte]

Dear FS experts,

I have shown in mailing list and xhemi commands as explained here, a
beginning of a solution to my problem :

http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi

However, I didn't understand all the steps needed in may case. I have
patients with unilateralized problem on left or right hemisphere. But, I
would like to statistically compare left vs right hemisphere groups. So, I
think xhemi should help me to register for example both hemispheres of my
right lateralized patients onto symmetrical template ?

I have already registered my surface data of all patients on fsaverage
template. Couldn't it be possible to apply Xhemi transformation on
fsaverage surface data of all right lateralized patients ? What are the
steps to do it ?

Many thanks in advance for helping !

Best regards,

Matthieu
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Re: [Freesurfer] Surface-based Cluster Summary Table as created by mri_glmfit-sim

[Matthieu Vanhoutte]

Some widespread clusters don't appear to be localized the place where is
the vertex with the maximum sig.

Best regards,

Matthieu
Le 21 août 2015 20:01, "Douglas Greve"  a écrit :

> It is based on the vertex with the maximum sig. What do you mean it does
> not fit well?
>
> On 8/19/15 1:25 PM, Matthieu Vanhoutte wrote:
> > Hello Freesurfer's experts,
> >
> > I used the group analysis clusterwise correction with glmfit-sim and I
> > found that "Annot" field in Cluster Summary Table don't always fit well
> > with the corresponding region on "?h.aparc.a2009s.annot" file.
> >
> > How is determined precisely each localization of each cluster in the
> > summary table ?
> >
> > Thanks in advance !
> >
> > Best regards,
> >
> > Matthieu
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] Surface-based Interhemispheric Registration : Compare left vs. right patients

[Matthieu Vanhoutte]

xhemireg seems to create e.g. left symmetric surface of the right normal
one. Once xhemi/surf/lh.pial has been created and surface data
surf/rh.overlay.mgh copied into xhemi/surf/lh.overlay.mgh, why don't
register surf/lh.overlay.mgh and xhemi/surf/lh.overlay onto fsaverage
lh.pial surface ?

Best regards,

Matthieu
Le 21 août 2015 19:49, "Douglas Greve"  a écrit :

>
> Sorry, what is the problem? Is sounds like xhemi should be apprpriate for
> your application.  fsaverage is not symmetric and will lead to biased
> results.
>
> On 8/20/15 9:27 AM, Matthieu Vanhoutte wrote:
>
> Dear FS experts,
>
> I have shown in mailing list and xhemi commands as explained here, a
> beginning of a solution to my problem :
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>
> However, I didn't understand all the steps needed in may case. I have
> patients with unilateralized problem on left or right hemisphere. But, I
> would like to statistically compare left vs right hemisphere groups. So, I
> think xhemi should help me to register for example both hemispheres of my
> right lateralized patients onto symmetrical template ?
>
> I have already registered my surface data of all patients on fsaverage
> template. Couldn't it be possible to apply Xhemi transformation on
> fsaverage surface data of all right lateralized patients ? What are the
> steps to do it ?
>
> Many thanks in advance for helping !
>
> Best regards,
>
> Matthieu
>
>
> ___
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Surface-based Cluster Summary Table as created by mri_glmfit-sim

[Matthieu Vanhoutte]

I upload you this day an exemple with number vertex with same title name.

Thanks in advance for helping !

Best regards,

Matthieu
Le 21 août 2015 23:57, "Douglas Greve"  a écrit :

> Can you upload an example (with vertex numbers)?
>
> On 8/21/15 3:37 PM, Matthieu Vanhoutte wrote:
>
> Some widespread clusters don't appear to be localized the place where is
> the vertex with the maximum sig.
>
> Best regards,
>
> Matthieu
> Le 21 août 2015 20:01, "Douglas Greve"  a
> écrit :
>
>> It is based on the vertex with the maximum sig. What do you mean it does
>> not fit well?
>>
>> On 8/19/15 1:25 PM, Matthieu Vanhoutte wrote:
>> > Hello Freesurfer's experts,
>> >
>> > I used the group analysis clusterwise correction with glmfit-sim and I
>> > found that "Annot" field in Cluster Summary Table don't always fit well
>> > with the corresponding region on "?h.aparc.a2009s.annot" file.
>> >
>> > How is determined precisely each localization of each cluster in the
>> > summary table ?
>> >
>> > Thanks in advance !
>> >
>> > Best regards,
>> >
>> > Matthieu
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>>
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>> is
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[Freesurfer] Error when loading ?h.aparc.annot on fsaverage_sym ?h.pial

[Matthieu Vanhoutte]

Dear Freesurfer experts,

It seems impossible to load ?h.aparc.annot annotation file on ?h.pial
surface of the fsaverage_sym subject. When I try under freeview, it crashes
and gives me this error :



























*Did not find any volume geometry information in the surfacepB
Did not find
any volume geometry information in the surfacepB
reading colortable from
annotation file...colortable with 1036 entries read (originally
/scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)[0]PETSC ERROR:
[0]PETSC
ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably
memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC

ERROR: or try http://valgrind.org  on linux or man
libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR:
configure using --with-debugging=yes, recompile, link, and run [0]PETSC
ERROR: to get more information on the crash.[0]PETSC ERROR:
- Error Message
[0]PETSC ERROR: Signal
received![0]PETSC ERROR:
[0]PETSC
ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008
HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124[0]PETSC ERROR: See
docs/changes/index.html for recent updates.[0]PETSC ERROR: See
docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See
docs/index.html for manual pages.[0]PETSC ERROR:
[0]PETSC
ERROR: Unknown Name on a linux-gnu named yakuza by matthieu Fri Aug 28
11:32:19 2015[0]PETSC ERROR: Libraries linked from
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt[0]PETSC
ERROR: Configure run at Tue Aug 10 15:01:59 2010[0]PETSC ERROR: Configure
options --with-debugging=no --with-cc=gcc --with-fc=g77
--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0
--with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3
FOPTFLAGS=-O3[0]PETSC ERROR:
[0]PETSC
ERROR: User provided function() line 0 in unknown directory unknown
file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59)
- process 0*
Could you help me please ?

Best regards,

Matthieu
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Re: [Freesurfer] Error when loading ?h.aparc.annot on fsaverage_sym ?h.pial

[Matthieu Vanhoutte]

I launched freeview, then added manually lh.pial and rh.pial of
fsaverage_sym. A this point all is OK.

Then it crashed when I try to load graphically lh.aparc.annot or
rh.aparc.annot. I viewed that in freesurfer mailing, this problem has been
told in the beginning of 2014 but nothing afterthen.

Do you have a comman line way to manage to load annotation file under
freeview ?

Matthieu

2015-08-28 16:42 GMT+02:00 Douglas Greve :

> what is your command line? Can you run it without the annotation?
>
>
> On 8/28/15 5:58 AM, Matthieu Vanhoutte wrote:
>
> Dear Freesurfer experts,
>
> It seems impossible to load ?h.aparc.annot annotation file on ?h.pial
> surface of the fsaverage_sym subject. When I try under freeview, it crashes
> and gives me this error :
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Did not find any volume geometry information in the surface pB Did not
> find any volume geometry information in the surface pB reading colortable
> from annotation file... colortable with 1036 entries read (originally
> /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range [0]PETSC ERROR: Try option
> -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> <http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC>
> ERROR: or try http://valgrind.org <http://valgrind.org> on linux or man
> libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR:
> configure using --with-debugging=yes, recompile, link, and run [0]PETSC
> ERROR: to get more information on the crash. [0]PETSC ERROR:
> - Error Message 
> [0]PETSC ERROR: Signal received! [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC
> ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See
> docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See
> docs/index.html for manual pages. [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named yakuza by matthieu Fri
> Aug 28 11:32:19 2015 [0]PETSC ERROR: Libraries linked from
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR:
> Configure options --with-debugging=no --with-cc=gcc --with-fc=g77
> --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0
> --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3
> FOPTFLAGS=-O3 [0]PETSC ERROR:
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file [unset]: aborting job: application called
> MPI_Abort(MPI_COMM_WORLD, 59) - process 0 *
> Could you help me please ?
>
> Best regards,
>
> Matthieu
>
>
> ___
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>
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> is
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Error when loading ?h.aparc.annot on fsaverage_sym ?h.pial

[Matthieu Vanhoutte]

Hello Bruce,

I try your command but freeview crashed with this message error :

freeview -f surf/lh.inflated:annot=label/lh.aparc.annot

























*Did not find any volume geometry information in the surfacepB
reading
colortable from annotation file...colortable with 1036 entries read
(originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)[0]PETSC
ERROR:
[0]PETSC
ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably
memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
<http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC>
ERROR: or try http://valgrind.org <http://valgrind.org> on linux or man
libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR:
configure using --with-debugging=yes, recompile, link, and run [0]PETSC
ERROR: to get more information on the crash.[0]PETSC ERROR:
- Error Message
[0]PETSC ERROR: Signal
received![0]PETSC ERROR:
[0]PETSC
ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008
HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124[0]PETSC ERROR: See
docs/changes/index.html for recent updates.[0]PETSC ERROR: See
docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See
docs/index.html for manual pages.[0]PETSC ERROR:
[0]PETSC
ERROR: Unknown Name on a linux-gnu named cube by matthieu Fri Aug 28
16:50:44 2015[0]PETSC ERROR: Libraries linked from
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt[0]PETSC
ERROR: Configure run at Tue Aug 10 15:01:59 2010[0]PETSC ERROR: Configure
options --with-debugging=no --with-cc=gcc --with-fc=g77
--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0
--with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3
FOPTFLAGS=-O3[0]PETSC ERROR:
[0]PETSC
ERROR: User provided function() line 0 in unknown directory unknown
file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59)
- process 0*

Best regards,

Matthieu

2015-08-28 17:05 GMT+02:00 Bruce Fischl :

> Hi Matthieu
>
> I believe you can use
>
> freeview -f lh.inflated:annot=lh.aparc.annot
>
>
> check out freeview -help. It lists this type of option
> cheers
> Bruce
>
> On Fri, 28 Aug 2015, Matthieu
> Vanhoutte wrote:
>
> > I launched freeview, then added manually lh.pial and rh.pial of
> > fsaverage_sym. A this point all is OK.
> >
> > Then it crashed when I try to load graphically lh.aparc.annot or
> > rh.aparc.annot. I viewed that in freesurfer mailing, this problem has
> been
> > told in the beginning of 2014 but nothing afterthen.
> >
> > Do you have a comman line way to manage to load annotation file under
> > freeview ?
> >
> > Matthieu
> >
> > 2015-08-28 16:42 GMT+02:00 Douglas Greve :
> >   what is your command line? Can you run it without the
> >   annotation?
> >
> >   On 8/28/15 5:58 AM, Matthieu Vanhoutte wrote:
> >   Dear Freesurfer experts,
> >
> > It seems impossible to load ?h.aparc.annot annotation file on
> > ?h.pial surface of the fsaverage_sym subject. When I try under
> > freeview, it crashes and gives me this error :
> >
> > Did not find any volume geometry information in the surface
> > pB Did not find any volume geometry information in the surface
> > pB reading colortable from annotation file...
> > colortable with 1036 entries read (originally
> > /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)
> > [0]PETSC ERROR:
> > 
> > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
> > Violation, probably memory access out of range
> > [0]PETSC ERROR: Try option -start_in_debugger or
> > -on_error_attach_debugger
> > [0]PETSC ERROR: or seehttp://
> www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si
> > gnal[0]PETSC ERROR: or try http://valgrind.org on linux or man
> > libgmalloc on Apple to find memory corruption errors
> > [0]PETSC ERROR: configure using --with-debugging=yes, recompile,
> > link, and run
> > [0]PETSC ERROR: to get more information on the crash.
> > [0]PETSC ERROR: - Error Message
> > ---

Re: [Freesurfer] Error when loading ?h.aparc.annot on fsaverage_sym ?h.pial

[Matthieu Vanhoutte]

I can do it. Where could I send you these files ?

Best regards,

Matthieu

2015-08-28 17:12 GMT+02:00 Ruopeng Wang :

> Would it be possible to send us lh.pial and lh.aparc.annot that caused the
> crash?
>
> Best,
> Ruopeng
>
> On Aug 28, 2015, at 10:59 AM, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> wrote:
>
> I launched freeview, then added manually lh.pial and rh.pial of
> fsaverage_sym. A this point all is OK.
>
> Then it crashed when I try to load graphically lh.aparc.annot or
> rh.aparc.annot. I viewed that in freesurfer mailing, this problem has been
> told in the beginning of 2014 but nothing afterthen.
>
> Do you have a comman line way to manage to load annotation file under
> freeview ?
>
> Matthieu
>
> 2015-08-28 16:42 GMT+02:00 Douglas Greve :
>
>> what is your command line? Can you run it without the annotation?
>>
>>
>> On 8/28/15 5:58 AM, Matthieu Vanhoutte wrote:
>>
>> Dear Freesurfer experts,
>>
>> It seems impossible to load ?h.aparc.annot annotation file on ?h.pial
>> surface of the fsaverage_sym subject. When I try under freeview, it crashes
>> and gives me this error :
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *Did not find any volume geometry information in the surface pB Did not
>> find any volume geometry information in the surface pB reading colortable
>> from annotation file... colortable with 1036 entries read (originally
>> /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) [0]PETSC ERROR:
>> 
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range [0]PETSC ERROR: Try option
>> -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>> <http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC>
>> ERROR: or try http://valgrind.org <http://valgrind.org/> on linux or man
>> libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR:
>> configure using --with-debugging=yes, recompile, link, and run [0]PETSC
>> ERROR: to get more information on the crash. [0]PETSC ERROR:
>> - Error Message 
>> [0]PETSC ERROR: Signal received! [0]PETSC ERROR:
>> 
>> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
>> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC
>> ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See
>> docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See
>> docs/index.html for manual pages. [0]PETSC ERROR:
>> 
>> [0]PETSC ERROR: Unknown Name on a linux-gnu named yakuza by matthieu Fri
>> Aug 28 11:32:19 2015 [0]PETSC ERROR: Libraries linked from
>> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
>> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR:
>> Configure options --with-debugging=no --with-cc=gcc --with-fc=g77
>> --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0
>> --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3
>> FOPTFLAGS=-O3 [0]PETSC ERROR:
>> 
>> [0]PETSC ERROR: User provided function() line 0 in unknown directory
>> unknown file [unset]: aborting job: application called
>> MPI_Abort(MPI_COMM_WORLD, 59) - process 0 *
>> Could you help me please ?
>>
>> Best regards,
>>
>> Matthieu
>>
>>
>> ___
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>>
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> conta

[Freesurfer] LME toolbox for longitudinal FA volume maps ?

[Matthieu Vanhoutte]

Dear experts,

I would like to know if it is possible to make a longitudinal study with
LME toolbox from volume FA maps registered in a common space ?

I don't have T1 images so the recon-all process couldn't be processed. But
if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels
format, could it be in good way for LME ?

Thanks for helping !

Best regards,

Matthieu
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Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

[Matthieu Vanhoutte]

Hi Martin,

Thank you for your answer.

However, I would like to consider FA maps as a mass-univariate problem and
not a univariate voxel-by-voxel as hippocampal volume. Indeed, my voxels
aren't independant, are they ? So, how to correct for multiple comparisons
then ?

Best regards,

Matthieu

2015-09-29 15:04 GMT+02:00 Martin Reuter :

> Hi Matthieu,
>
> if all your images are perfectly registered, you can do LME on a
> voxel-by-voxel basis, just as if you had hippocampal volume or any other
> ROI measure.
>
> Best, Martin
>
>
> On 09/29/2015 06:46 AM, Matthieu Vanhoutte wrote:
>
> Dear experts,
>
> I would like to know if it is possible to make a longitudinal study with
> LME toolbox from volume FA maps registered in a common space ?
>
> I don't have T1 images so the recon-all process couldn't be processed. But
> if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels
> format, could it be in good way for LME ?
>
> Thanks for helping !
>
> Best regards,
>
> Matthieu
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  : http://reuter.mit.edu
>
>
> ___
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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> properly
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Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

[Matthieu Vanhoutte]

Hi Martin,

I understand for the multiple comparisons problem. But if I consider a
voxel-by-voxel analysis just as hippocampal volume (lme_fit_FS for
estimation), how could I consider a correction for multiple comparisons in
this univariate case ?

Shouldn't I use the lme_mass_fit or lme_mass_fit_vw functions in my mass
univariate case ? If yes, how do I have to format my 3D FA volume as input
of the LME toolbox ?

Best regards,

Matthieu

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-09-29 16:34 GMT+02:00 Martin Reuter :

> Hi Matthieu,
>
> yes, multiple comparisons are a problem for any mass univariate approach.
> You can use the FDR2 correction (in the lme matlab tools) which is less
> conservative than standard FDR. You can also work in specific ROI's and
> average there, to reduce the number of comparisons.
>
> Best, Martin
>
>
> On 09/29/2015 09:11 AM, Matthieu Vanhoutte wrote:
>
> Hi Martin,
>
> Thank you for your answer.
>
> However, I would like to consider FA maps as a mass-univariate problem and
> not a univariate voxel-by-voxel as hippocampal volume. Indeed, my voxels
> aren't independant, are they ? So, how to correct for multiple comparisons
> then ?
>
> Best regards,
>
> Matthieu
>
> 2015-09-29 15:04 GMT+02:00 Martin Reuter :
>
>> Hi Matthieu,
>>
>> if all your images are perfectly registered, you can do LME on a
>> voxel-by-voxel basis, just as if you had hippocampal volume or any other
>> ROI measure.
>>
>> Best, Martin
>>
>>
>> On 09/29/2015 06:46 AM, Matthieu Vanhoutte wrote:
>>
>> Dear experts,
>>
>> I would like to know if it is possible to make a longitudinal study with
>> LME toolbox from volume FA maps registered in a common space ?
>>
>> I don't have T1 images so the recon-all process couldn't be processed.
>> But if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels
>> format, could it be in good way for LME ?
>>
>> Thanks for helping !
>>
>> Best regards,
>>
>> Matthieu
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> Martin Reuter, PhD
>> Assistant Professor of Radiology, Harvard Medical School
>> Assistant Professor of Neurology, Harvard Medical School
>> A.A.Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> Research Affiliate, CSAIL, MIT
>> Phone: +1-617-724-5652
>> Web  : http://reuter.mit.edu
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  : http://reuter.mit.edu
>
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

[Matthieu Vanhoutte]

Hi Martin,

Thank you for helping !

1) What should I use for the parameter estimation: "mass univariate" or Novel
mass-univariate tools (spatiotemporal models)" ?

2) I have one group of subjects with different timepoints (non equally
spaced and different numbers of timepoints), and would like to see the
significant change of FA according to time. Will LME study allow me to get
this change and how to define contrast to assess it ? Are the results of
this longitudinal study directionals, i.e. is it possible to establish an
increase or decrease of FA in significant regions according to time ?

3) Should the covariates (age, gender...) be demeaned or centered ?

4) Has the accurate time variable to be in years absolutely or could it be
also in days ?


Best regards,

Matthieu


2015-09-29 17:11 GMT+02:00 Martin Reuter :

> Hi Matthieu,
>
> use lme_mass_fit_vw and the y is a simple vector. I would mask the image
> before doing this and only pass the brain voxels (to increase speed and
> reduce comparisons).
>
> Best, Martin
>
>
> On 09/29/2015 10:43 AM, Matthieu Vanhoutte wrote:
>
> Hi Martin,
>
> I understand for the multiple comparisons problem. But if I consider a
> voxel-by-voxel analysis just as hippocampal volume (lme_fit_FS for
> estimation), how could I consider a correction for multiple comparisons in
> this univariate case ?
>
> Shouldn't I use the lme_mass_fit or lme_mass_fit_vw functions in my mass
> univariate case ? If yes, how do I have to format my 3D FA volume as input
> of the LME toolbox ?
>
> Best regards,
>
> Matthieu
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-09-29 16:34 GMT+02:00 Martin Reuter :
>
>> Hi Matthieu,
>>
>> yes, multiple comparisons are a problem for any mass univariate approach.
>> You can use the FDR2 correction (in the lme matlab tools) which is less
>> conservative than standard FDR. You can also work in specific ROI's and
>> average there, to reduce the number of comparisons.
>>
>> Best, Martin
>>
>>
>> On 09/29/2015 09:11 AM, Matthieu Vanhoutte wrote:
>>
>> Hi Martin,
>>
>> Thank you for your answer.
>>
>> However, I would like to consider FA maps as a mass-univariate problem
>> and not a univariate voxel-by-voxel as hippocampal volume. Indeed, my
>> voxels aren't independant, are they ? So, how to correct for multiple
>> comparisons then ?
>>
>> Best regards,
>>
>> Matthieu
>>
>> 2015-09-29 15:04 GMT+02:00 Martin Reuter :
>>
>>> Hi Matthieu,
>>>
>>> if all your images are perfectly registered, you can do LME on a
>>> voxel-by-voxel basis, just as if you had hippocampal volume or any other
>>> ROI measure.
>>>
>>> Best, Martin
>>>
>>>
>>> On 09/29/2015 06:46 AM, Matthieu Vanhoutte wrote:
>>>
>>> Dear experts,
>>>
>>> I would like to know if it is possible to make a longitudinal study with
>>> LME toolbox from volume FA maps registered in a common space ?
>>>
>>> I don't have T1 images so the recon-all process couldn't be processed.
>>> But if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels
>>> format, could it be in good way for LME ?
>>>
>>> Thanks for helping !
>>>
>>> Best regards,
>>>
>>> Matthieu
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> --
>>> Martin Reuter, PhD
>>> Assistant Professor of Radiology, Harvard Medical School
>>> Assistant Professor of Neurology, Harvard Medical School
>>> A.A.Martinos Center for Biomedical Imaging
>>> Massachusetts General Hospital
>>> Research Affiliate, CSAIL, MIT
>>> Phone: +1-617-724-5652
>>> Web  : http://reuter.mit.edu
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains pati

[Freesurfer] QA Tools : All in errors for aseg outliers detection

[Matthieu Vanhoutte]

Dear FS experts,

I tried to run the QA Tools on a subject with the following command:
*${QA_TOOLS}/recon_checker -s 207043_M0_2010-10-07 -outputFOF
${SUBJECTS_DIR}/FOF -gen-outputFOF -gen-asegLUT
${SUBJECTS_DIR}/AsegOutliers*

But I got all errors concerning the detection of Aseg outliers:
*Making aseg look-up table, /NAS/tupac/matthieu/FS5.3//AsegOutliers*
*parsing arguments ...*
*checking parameters ...*
*MeanFile is /NAS/tupac/matthieu/FS5.3//AsegOutliers*
*checking logs ...*
*done checking logs ...*
*done checking parameters ...*
*moving previous log files to *.bak*
*done moving previous log files*
*Processing each subcortical label ...*
*(standard_in) 1: syntax error*
*gawk: /home/matthieu/programs/QAtools_v1.1/gstd.awk:22: (FILENAME=- FNR=1)
fatal: division by zero attempted*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*




*-Checking asegs for outliers...Using asegLUT:
/NAS/tupac/matthieu/FS5.3//AsegOutliersparsing arguments ...checking
parameters ...checking logs ...done checking logs ...done checking
parameters ...moving previous log files to *.bakdone moving previous log
filesProcessing each subcortical label ...(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error*
Please find attached the recon_checker summary.

Thanks in advance for any help !

Best regards,
Matthieu

Tue Jun 14 11:07:11 CEST 2016


SUBJECTS_DIR: /NAS/tupac/matthieu/FS5.3/ 

Generating file order list using subject 207043_M0_2010-10-07
 Using file list: /NAS/tupac/matthieu/FS5.3//QA/local_default_output_order_file


checking subcortical label: Left-Cerebral-Exterior, 0 +/-
checking subcortical label: Left-Cerebral-White-Matter, 0 +/-
checking subcortical label: Left-Cerebral-Cortex, 0 +/-
checking subcortical label: Left-Lateral-Ventricle, 0 +/-
checking subcortical label: Left-Inf-Lat-Vent, 0 +/-
checking subcortical label: Left-Cerebellum-Exterior, 0 +/-
checking subcortical label: Left-Cerebellum-White-Matter, 0 +/-
checking subcortical label: Left-Cerebellum-Cortex, 0 +/-
checking subcortical label: Left-Thalamus, 0 +/-
checking subcortical label: Left-Thalamus-Proper, 0 +/-
checking subcortical label: Left-Caudate, 0 +/-
checking subcortical label: Left-Putamen, 0 +/-
checking subcortical label: Left-Pallidum, 0 +/-
checking subcortical label: 3rd-Ventricle, 0 +/-
checking subcortical label: 4th-Ventricle, 0 +/-
checking subcortical label: Brain-Stem, 0 +/-
checking subcortical label: Left-Hippocampus, 0 +/-
checking subcortical label: Left-Amygdala, 0 +/-
checking subcortical label: Left-Insula, 0 +/-
checking subcortical label: Left-Operculum, 0 +/-
checking subcortical label: Line-1, 0 +/-
checking subcortical label: Line-2, 

[Freesurfer] Interpretation of QA tools results

[Matthieu Vanhoutte]

Dear FS experts,

Could you explained me how to interpret results from the QA tools. Please
find attached the recon_checker summary log.

1) How to know there is a problem according to results below:

*checking subcortical label: Left-Cerebral-Exterior, 0 +/-*
*checking subcortical label: Left-Cerebral-White-Matter, 0 +/-*
*checking subcortical label: Left-Cerebral-Cortex, 0 +/-*
*checking subcortical label: Left-Lateral-Ventricle, 1.77932 +/-*
*checking subcortical label: Left-Inf-Lat-Vent, 0.115084 +/-*
*checking subcortical label: Left-Cerebellum-Exterior, 0 +/-*
*checking subcortical label: Left-Cerebellum-White-Matter, 0.768042 +/-*
*checking subcortical label: Left-Cerebellum-Cortex, 2.50118 +/-*
*checking subcortical label: Left-Thalamus, 0 +/-*
*checking subcortical label: Left-Thalamus-Proper, 0.324235 +/-*
*checking subcortical label: Left-Caudate, 0.190688 +/-*
*checking subcortical label: Left-Putamen, 0.24631 +/-*
*checking subcortical label: Left-Pallidum, 0.0782828 +/-*
*checking subcortical label: 3rd-Ventricle, 0.127606 +/-*
*checking subcortical label: 4th-Ventricle, 0.0697322 +/-*
*checking subcortical label: Brain-Stem, 1.2108 +/-*
*checking subcortical label: Left-Hippocampus, 0.191568 +/-*
*checking subcortical label: Left-Amygdala, 0.0665945 +/-*
*checking subcortical label: Left-Insula, 0 +/-*
*checking subcortical label: Left-Operculum, 0 +/-*
*checking subcortical label: Line-1, 0 +/-*
*checking subcortical label: Line-2, 0 +/-*
*checking subcortical label: Line-3, 0 +/-*
*checking subcortical label: CSF, 0.0903738 +/-*
*checking subcortical label: Left-Lesion, 0 +/-*
*checking subcortical label: Left-Accumbens-area, 0.0259807 +/-*
*checking subcortical label: Left-Substancia-Nigra, 0 +/-*
*checking subcortical label: Left-VentralDC, 0.196737 +/-*
*checking subcortical label: Left-undetermined, 0 +/-*
*checking subcortical label: Left-vessel, 0.0043689 +/-*
*checking subcortical label: Left-choroid-plexus, 0.0806885 +/-*

2) When looking at the white matter QA, three colors are used: red (pial
surface ?), yellow (white surface ?) and green (?). Does it make sense to
verify all colored surfaces or only the white matter surface in this WM QA ?
How to decide when rejecting bad preprocessed subject ?

Best regards,
Matthieu

Tue Jun 14 11:34:52 CEST 2016


SUBJECTS_DIR: /NAS/tupac/matthieu/FS5.3/ 

Generating file order list using subject 207043_M0_2010-10-07
 Using file list: /NAS/tupac/matthieu/FS5.3//QA/local_default_output_order_file


checking subcortical label: Left-Cerebral-Exterior, 0 +/-
checking subcortical label: Left-Cerebral-White-Matter, 0 +/-
checking subcortical label: Left-Cerebral-Cortex, 0 +/-
checking subcortical label: Left-Lateral-Ventricle, 1.77932 +/-
checking subcortical label: Left-Inf-Lat-Vent, 0.115084 +/-
checking subcortical label: Left-Cerebellum-Exterior, 0 +/-
checking subcortical label: Left-Cerebellum-White-Matter, 0.768042 +/-
checking subcortical label: Left-Cerebellum-Cortex, 2.50118 +/-
checking subcortical label: Left-Thalamus, 0 +/-
checking subcortical label: Left-Thalamus-Proper, 0.324235 +/-
checking subcortical label: Left-Caudate, 0.190688 +/-
checking subcortical label: Left-Putamen, 0.24631 +/-
checking subcortical label: Left-Pallidum, 0.0782828 +/-
checking subcortical label: 3rd-Ventricle, 0.127606 +/-
checking subcortical label: 4th-Ventricle, 0.0697322 +/-
checking subcortical label: Brain-Stem, 1.2108 +/-
checking subcortical label: Left-Hippocampus, 0.191568 +/-
checking subcortical label: Left-Amygdala, 0.0665945 +/-
checking subcortical label: Left-Insula, 0 +/-
checking subcortical label: Left-Operculum, 0 +/-
checking subcortical label: Line-1, 0 +/-
checking subcortical label: Line-2, 0 +/-
checking subcortical label: Line-3, 0 +/-
checking subcortical label: CSF, 0.0903738 +/-
checking subcortical label: Left-Lesion, 0 +/-
checking subcortical label: Left-Accumbens-area, 0.0259807 +/-
checking subcortical label: Left-Substancia-Nigra, 0 +/-
checking subcortical label: Left-VentralDC, 0.196737 +/-
checking subcortical label: Left-undetermined, 0 +/-
checking subcortical label: Left-vessel, 0.0043689 +/-
checking subcortical label: Left-choroid-plexus, 0.0806885 +/-
checking subcortical label: Left-F3orb, 0 +/-
checking subcortical label: Left-lOg, 0 +/-
checking subcortical label: Left-aOg, 0 +/-
checking subcortical label: Left-mOg, 0 +/-
checking subcortical label: Left-pOg, 0 +/-
checking subcortical label: Left-Stellate, 0 +/-
checking subcortical label: Left-Porg, 0 +/-
checking subcortical label: Left-Aorg, 0 +/-
checking subcortical label: Right-Cerebral-Exterior, 0 +/-
checking subcortical label: Right-Cerebral-White-Matter, 0 +/-
checking subcortical label: Right-Cerebral-Cortex, 0 +/-
checking subcortical label: Right-Lateral-Ventricle, 1.19538 +/-
checking subcortical label: Right-Inf-Lat-Vent, 0.0696698 +/-
checking subcortical label: Right-Cerebellum-Exterior, 0 +/-
checking su

[Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Dear experts,

I am in trouble with two ways of computing mean intensity with mri_segstats.

First I have used on .annot files with three different labels inside (SegId
1 to 3) :

*mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i
lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum*

which give me those results:
# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max
Range
  1   1 2780514182.6  cluster-0018.8194
1.4351 6.210514.2947 8.0842
  2   2  2321 1047.3  cluster-002   10.3661
1.0848 8.837512.9317 4.0942
  3   3   552  313.1  cluster3  10.3365
0.4711 9.371911.8694 2.4975

Second I have created on .label files containing the three segmented labels
(SegId 1 to 3) and used this label with mri_segstats:

*mri_segstats --slabel fsaverage lh lh.th23.cluster.thresh1.3.label --i
lh.PET.fsaverage.sm10.mgh --excludeid 0 --sum lh.pet.label.sum *

which give me those results:
*# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
Max Range  *
*  1   1 3067815542.9  Seg0001 8.9637 1.4701 6.2105
 14.2947 8.0842 *

I verified if I obtained the same results with the two ways (.annot or
.label) and everything is fine comparing NVertices, Area_mm2 but Mean in
first way gives me (8.8194+10.3661+10.3365)/3 = 9.84066 and with .label
file Mean = 8.9637.

Did I have miss anything and how is computed mean intensity ?

Many thanks in advance.

Best regards,
Matthieu
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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Hello FS's experts,

Would anyone have an advice for my problem ?

Best regards,
Matthieu

2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte :

> Dear experts,
>
> I am in trouble with two ways of computing mean intensity with
> mri_segstats.
>
> First I have used on .annot files with three different labels inside
> (SegId 1 to 3) :
>
> *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i
> lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum*
>
> which give me those results:
> # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
> Max Range
>   1   1 2780514182.6  cluster-0018.8194
>   1.4351 6.210514.2947 8.0842
>   2   2  2321 1047.3  cluster-002   10.3661
>   1.0848 8.837512.9317 4.0942
>   3   3   552  313.1  cluster3  10.3365
>   0.4711 9.371911.8694 2.4975
>
> Second I have created on .label files containing the three segmented
> labels (SegId 1 to 3) and used this label with mri_segstats:
>
> *mri_segstats --slabel fsaverage lh lh.th23.cluster.thresh1.3.label --i
> lh.PET.fsaverage.sm10.mgh --excludeid 0 --sum lh.pet.label.sum *
>
> which give me those results:
> *# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
> Max Range  *
> *  1   1 3067815542.9  Seg0001 8.9637 1.4701 6.2105
>  14.2947 8.0842 *
>
> I verified if I obtained the same results with the two ways (.annot or
> .label) and everything is fine comparing NVertices, Area_mm2 but Mean in
> first way gives me (8.8194+10.3661+10.3365)/3 = 9.84066 and with .label
> file Mean = 8.9637.
>
> Did I have miss anything and how is computed mean intensity ?
>
> Many thanks in advance.
>
> Best regards,
> Matthieu
>
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[Freesurfer] Longitudinal surface analysis of PET data

[Matthieu Vanhoutte]

Dear Freesurfer’s experts,

I would like to use the longitudinal mixed-effects model for surface PET 
analysis. Although I could find all the process to follow the longitudinal 
analysis of cortical thickness, I couldn’t resolve the steps/commands to apply 
successively to coregistered PET data on T1 MRI.

Could you precise me the process and commands to use for PET longitudinal 
analysis ?

Many thanks in advance !

Best regards,
Matthieu
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Re: [Freesurfer] Longitudinal surface analysis of PET data

[Matthieu Vanhoutte]

Hi Martin,

Thanks for your answer. However, it seems to me that cortical thickness follow 
a particular process with the recon-all -long process, isn’t it ? Is there any 
resample onto average time subject then other operation following ?

Best regards,
Matthieu

> Le 18 sept. 2016 à 16:26, Martin Reuter  a écrit 
> :
> 
> Hi Matthieu,
> 
> I never used PET data, but once you manage to resample you pet data onto the 
> surface, you will have a file similar to the thickness file for each 
> subjects. Instead of thickness it holds you PET information. From that point 
> on everything should be identical to the thickness analysis.
> 
> So this is really more a question how to get your PET data sampled onto the 
> surface. If no one else replies, write that into the subject line and repost. 
> 
> Best, Martin
> 
> 
>> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte 
>>  wrote:
>> 
>> Dear Freesurfer’s experts,
>> 
>> I would like to use the longitudinal mixed-effects model for surface PET 
>> analysis. Although I could find all the process to follow the longitudinal 
>> analysis of cortical thickness, I couldn’t resolve the steps/commands to 
>> apply successively to coregistered PET data on T1 MRI.
>> 
>> Could you precise me the process and commands to use for PET longitudinal 
>> analysis ?
>> 
>> Many thanks in advance !
>> 
>> Best regards,
>> Matthieu
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
> 
> 
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
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Re: [Freesurfer] Longitudinal surface analysis of PET data

[Matthieu Vanhoutte]

Dear Freesurfer's experts,

Could you answer me about my last question with no response in the mail
below ?

When using cortical thickness in longitudinal analysis with LME, we used
lh.thickness or rh.thickness from -long subject directories. These data
followed particular processing steps including registrations in order to
use them with more precision in longitudinal studies, didn't they ?

My problem is that I would like to perform longitudinal study on PET data
images with LME. So I wonder if I just have to resample onto -long cortical
subject surface ? Do I need to follow the same steps than cortical
thickness from cross-sectional to -long subject directories ? If this is
the case, which commands should I use to mimic cortical thickness
longitudinal data ?

Many thanks in advance for helping !

Best regards,
Matthieu

2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte :

> Hi Martin,
>
> Thanks for your answer. However, it seems to me that cortical thickness
> follow a particular process with the recon-all -long process, isn’t it ? Is
> there any resample onto average time subject then other operation following
> ?
>
> Best regards,
> Matthieu
>
> > Le 18 sept. 2016 à 16:26, Martin Reuter  a
> écrit :
> >
> > Hi Matthieu,
> >
> > I never used PET data, but once you manage to resample you pet data onto
> the surface, you will have a file similar to the thickness file for each
> subjects. Instead of thickness it holds you PET information. From that
> point on everything should be identical to the thickness analysis.
> >
> > So this is really more a question how to get your PET data sampled onto
> the surface. If no one else replies, write that into the subject line and
> repost.
> >
> > Best, Martin
> >
> >
> >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> wrote:
> >>
> >> Dear Freesurfer’s experts,
> >>
> >> I would like to use the longitudinal mixed-effects model for surface
> PET analysis. Although I could find all the process to follow the
> longitudinal analysis of cortical thickness, I couldn’t resolve the
> steps/commands to apply successively to coregistered PET data on T1 MRI.
> >>
> >> Could you precise me the process and commands to use for PET
> longitudinal analysis ?
> >>
> >> Many thanks in advance !
> >>
> >> Best regards,
> >> Matthieu
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> > contains patient information, please contact the Partners Compliance
> HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

[Matthieu Vanhoutte]

Dear Freesurfer's experts,

I would like to register PET image onto T1 anatomical. I used bbregister
with the following command and it failed :
*bbregister  --s SUBJID --init-fsl --t2 --mov PET.nii.gz --reg
Pet2T1.register.dof6.dat --lta Pet2T1.register.dof6.lta --init-reg-out
Pet2T1.init.register.dof6.dat --o rPET.nii.gz *

Having heard about mri_coreg solving some bbregister fails, I tested it
with the following command :
*mri_coreg --s SUBJID  --mov PET.nii.gz --reg
Pet2T1.register.dof6.mri_coreg.lta --regdat
Pet2T1.register.dof6.mri_coreg.dat*

But it failed in the same way than bbregister. Do you have any advice on
this problem ?

Best regards,
Matthieu
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Longitudinal surface analysis of PET data

[Matthieu Vanhoutte]

Hi Douglas,

Does the surface of the closest MRI time point mean the surface of the
-long subject time point directory rather than cross-sectional subject time
point directory ?

Best regards,
Matthieu

Le 30 sept. 2016 9:14 PM, "Douglas N Greve"  a
écrit :

> There is no such long process for PET. The idea is that you process the
> MRI in a longitudinal way, then sample the PET data onto the surface of
> the closest MRI time point. Then proceed in a way similar to the
> thickness analysis
>
>
> On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote:
> > Dear Freesurfer's experts,
> >
> > Could you answer me about my last question with no response in the
> > mail below ?
> >
> > When using cortical thickness in longitudinal analysis with LME, we
> > used lh.thickness or rh.thickness from -long subject directories.
> > These data followed particular processing steps including
> > registrations in order to use them with more precision in longitudinal
> > studies, didn't they ?
> >
> > My problem is that I would like to perform longitudinal study on PET
> > data images with LME. So I wonder if I just have to resample onto
> > -long cortical subject surface ? Do I need to follow the same steps
> > than cortical thickness from cross-sectional to -long subject
> > directories ? If this is the case, which commands should I use to
> > mimic cortical thickness longitudinal data ?
> >
> > Many thanks in advance for helping !
> >
> > Best regards,
> > Matthieu
> >
> > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte
> > mailto:matthieuvanhou...@gmail.com>>:
> >
> > Hi Martin,
> >
> > Thanks for your answer. However, it seems to me that cortical
> > thickness follow a particular process with the recon-all -long
> > process, isn’t it ? Is there any resample onto average time
> > subject then other operation following ?
> >
> > Best regards,
> > Matthieu
> >
> > > Le 18 sept. 2016 à 16:26, Martin Reuter
> > mailto:mreu...@nmr.mgh.harvard.edu>>
> > a écrit :
> > >
> > > Hi Matthieu,
> > >
> > > I never used PET data, but once you manage to resample you pet
> > data onto the surface, you will have a file similar to the
> > thickness file for each subjects. Instead of thickness it holds
> > you PET information. From that point on everything should be
> > identical to the thickness analysis.
> > >
> > > So this is really more a question how to get your PET data
> > sampled onto the surface. If no one else replies, write that into
> > the subject line and repost.
> > >
> > > Best, Martin
> > >
> > >
> > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte
> > mailto:matthieuvanhou...@gmail.com>>
> > wrote:
> > >>
> > >> Dear Freesurfer’s experts,
> > >>
> > >> I would like to use the longitudinal mixed-effects model for
> > surface PET analysis. Although I could find all the process to
> > follow the longitudinal analysis of cortical thickness, I couldn’t
> > resolve the steps/commands to apply successively to coregistered
> > PET data on T1 MRI.
> > >>
> > >> Could you precise me the process and commands to use for PET
> > longitudinal analysis ?
> > >>
> > >> Many thanks in advance !
> > >>
> > >> Best regards,
> > >> Matthieu
> > >> ___
> > >> Freesurfer mailing list
> > >> Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> > >>
> > >>
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> > >
> > >
> > > The information in this e-mail is intended only for the person
> > to whom it is
> > > addressed. If you b

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

[Matthieu Vanhoutte]

 -0.13577
-1.0287210*
*#@#  2  657  3.09369 15.04550 68.21119 7.08699 0.02114 0.86423
-1.0287254*
*  powell nthiter 1: fret = -1.028725*
*#@#  2  681  3.12473 15.04550 68.21119 7.08699 0.02114 0.95289
-1.0287255*
*#@#  2  695  3.12664 15.42746 68.21119 7.08699 0.02114 0.95289
-1.0287271*
*#@#  2  696  3.12664 15.34841 68.21119 7.08699 0.02114 0.95289
-1.0287273*
*#@#  2  720  3.12664 15.32519 68.20757 7.08297 0.02114 0.95289
-1.0287274*
*#@#  2  724  3.12664 15.32519 68.20757 7.07547 0.02114 0.95289
-1.0287275*
*#@#  2  745  3.12664 15.32519 68.20757 7.07447 0.01759 0.81959
-1.0287278*
*#@#  2  762  3.14700 15.49804 68.20535 7.06672 0.01540 0.72493
-1.0287280*
*  powell nthiter 2: fret = -1.028728*
*#@#  2  792  3.14765 15.49494 68.20538 7.06686 0.01544 0.59641
-1.0287281*
*#@#  2  803  3.14765 15.49494 68.11650 7.06686 0.01544 0.59810
-1.0287282*
*#@#  2  804  3.14765 15.49494 68.14099 7.06686 0.01544 0.59810
-1.0287284*
*#@#  2  805  3.14765 15.49494 68.15399 7.06686 0.01544 0.59810
-1.0287285*
*#@#  2  807  3.14765 15.49494 68.16380 7.06686 0.01544 0.59810
-1.0287286*
*  powell nthiter 3: fret = -1.028729*
*#@#  2  867  3.12259 15.49539 68.16066 7.07157 0.0 0.59788
-1.0287287*
*Powell done niters total = 4*
*OptTimeSec 161.2 sec*
*OptTimeMin  2.69 min*
*nEvals 938*
*Final parameters   3.12265301  15.49595165  68.16065216   7.06536150
0.01209922   0.59759676 *
*Final cost   -1.028728664232616*


*-*
*mri_coreg utimesec241.181825*
*mri_coreg stimesec0.360032*
*mri_coreg ru_maxrss   504732*
*mri_coreg ru_ixrss0*
*mri_coreg ru_idrss0*
*mri_coreg ru_isrss0*
*mri_coreg ru_minflt   381121*
*mri_coreg ru_majflt   0*
*mri_coreg ru_nswap0*
*mri_coreg ru_inblock  71512*
*mri_coreg ru_oublock  16*
*mri_coreg ru_msgsnd   0*
*mri_coreg ru_msgrcv   0*
*mri_coreg ru_nsignals 0*
*mri_coreg ru_nvcsw505*
*mri_coreg ru_nivcsw   28383*
*Final  RefRAS-to-MovRAS*
* 0.5   0.01043   0.00021   3.12265;*
*-0.01038   0.99235   0.12300   15.49595;*
* 0.00107  -0.12300   0.99241   68.16065;*
* 0.0   0.0   0.0   1.0;*
*Final  RefVox-to-MovVox*
* 0.5   0.00021  -0.01043   19.00880;*
*-0.01038   0.12300  -0.99235   243.54027;*
*-0.00107  -0.99241  -0.12300   188.07765;*
* 0.0   0.0   0.0   1.0;*
*Final parameters  3.1227 15.4960 68.1607  7.0654  0.0121  0.5976 *
*nhits = 1287172 out of 16777216, Percent Overlap:  61.4*
*mri_coreg RunTimeSec 241.7 sec*
*To check run:*
*   tkregisterfv --mov BS7_PET.lps.nii.gz --targ
/NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/brainmask.mgz --reg
Pet2T1.BS7.register.dof6.mri_coreg.lta --s 207118_M0_2014-01-29 --surfs *

*mri_coreg done*


Best regards,
Matthieu

2016-09-30 21:07 GMT+02:00 Douglas N Greve :

> Can you send the mri_coreg terminal output?
>
>
> On 09/29/2016 11:19 AM, Matthieu Vanhoutte wrote:
> > Dear Freesurfer's experts,
> >
> > I would like to register PET image onto T1 anatomical. I used
> > bbregister with the following command and it failed :
> > /bbregister  --s SUBJID --init-fsl --t2 --mov PET.nii.gz --reg
> > Pet2T1.register.dof6.dat --lta Pet2T1.register.dof6.lta --init-reg-out
> > Pet2T1.init.register.dof6.dat --o rPET.nii.gz /
> > /
> > /
> > Having heard about mri_coreg solving some bbregister fails, I tested
> > it with the following command :
> > /mri_coreg --s SUBJID  --mov PET.nii.gz --reg
> > Pet2T1.register.dof6.mri_coreg.lta --regdat
> > Pet2T1.register.dof6.mri_coreg.dat/
> > /
> > /
> > But it failed in the same way than bbregister. Do you have any advice
> > on this problem ?
> >
> > Best regards,
> > Matthieu
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, ple

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

[Matthieu Vanhoutte]

Hi Douglas,

I have just sent it to you on Filedrop.

Best regards,
Matthieu

2016-10-03 17:45 GMT+02:00 Douglas Greve :

> Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to
> me on our filedrop?
>
> On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote:
>
> Hi Douglas,
>
> Please find below the mri_coreg terminal output :
>
> *$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $*
> *cwd /NAS/tupac/matthieu/FS5.3/207118_M0_2014-01-29/pet*
> *cmdline mri_coreg --s 207118_M0_2014-01-29 --mov BS7_PET.lps.nii.gz --reg
> Pet2T1.BS7.register.dof6.mri_coreg.lta --regdat
> Pet2T1.BS7.register.dof6.mri_coreg.dat *
> *sysname  Linux*
> *hostname yakuza*
> *machine  x86_64*
> *user matthieu*
> *dof6*
> *nsep2*
> *cras01*
> *ftol0.00*
> *linmintol0.001000*
> *bf   1*
> *bflim30.00*
> *bfnsamp30*
> *SmoothRef 0*
> *SatPct99.99*
> *MovOOB 0*
> *optschema 1*
> *Reading in mov BS7_PET.lps.nii.gz*
> *Reading in ref
> /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/brainmask.mgz*
> *Reading in and applying refmask
> /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/aparc+aseg.mgz*
> *Setting cras translation parameters to align centers*
> *Creating random numbers for coordinate dithering*
> *Performing intensity dithering*
> *Initial parameters 20.9141 11.8161 149.1538  0.  0.  0.
>  1.  1.  1.  0.  0.  0. *
> *Separation list (2):  4  2   min = 2*
> *DoSmoothing 1*
> *DoCoordDither 1*
> *DoIntensityDither 1*
> *nitersmax 4*
> *ftol 1.000e-07*
> *linmintol 1.000e-03*
> *SatPct 99.99*
> *Hist FWHM 7.00 7.00*
> *nthreads 1*
> *movsat = 10897.7666*
> *mov gstd 0.8459 0.8459 0.8459*
> *Smoothing mov*
> *refsat = 119.*
> *ref gstd 0.8459 0.8459 0.8459*
> *Smoothing ref*
> *COREGpreproc() done*
> *Testing if mov and target overlap*
> *Init cost   -1.0011578057*
> *nhits = 262144 out of 16777216, Percent Overlap: 100.0*
> *Initial  RefRAS-to-MovRAS*
> * 1.0   0.0   0.0   20.91408;*
> * 0.0   1.0   0.0   11.81612;*
> * 0.0   0.0   1.0   149.15384;*
> * 0.0   0.0   0.0   1.0;*
> *Initial  RefVox-to-MovVox*
> * 1.0   0.0   0.0   0.0;*
> * 0.0   0.0  -1.0   255.0;*
> * 0.0  -1.0   0.0   255.0;*
> * 0.0   0.0   0.0   1.0;*
> *sep = 4 ---*
> *COREGoptBruteForce() 30 1 30*
> *Turning on MovOOB for BruteForce Search*
> *#BF# sep= 4 iter=0 lim=30.0 delta=2.00   4.91408  21.81612 119.15384
> 2.0   0.0   0.0   -1.0078773*
> *Turning  MovOOB back off after brute force search*
>
>
> *-*
> *Init Powel Params dof = 6*
> *Starting OpenPowel2(), sep = 4*
> *InitialCost-1.0076701641 *
> *#@#  4  188  4.91408 21.81612 119.15384 2.0 0.0 0.0
> -1.0076702*
> *fs_powell::minimize*
> *  nparams 6*
> *  maxfev 4*
> *  ftol   0.00*
> *  linmin_xtol_   0.001000*
> *  powell nthiter 0: fret = -1.007670*
> *#@#  4  197  4.93866 21.81612 119.15384 2.0 0.0 0.0
> -1.0076704*
> *#@#  4  198  4.96905 21.81612 119.15384 2.0 0.0 0.0
> -1.0076705*
> *#@#  4  209  4.97536 20.19808 119.15384 2.0 0.0 0.0
> -1.0077189*
> *#@#  4  210  4.97536 19.55424 119.15384 2.0 0.0 0.0
> -1.0077529*
> *#@#  4  211  4.97536 18.51247 119.15384 2.0 0.0 0.0
> -1.0078081*
> *#@#  4  212  4.97536 16.82685 119.15384 2.0 0.0 0.0
> -1.0078434*
> *#@#  4  213  4.97536 16.77889 119.15384 2.0 0.0 0.0
> -1.0078460*
> *#@#  4  214  4.97536 16.70129 119.15384 2.0 0.0 0.0
> -1.0078515*
> *#@#  4  215  4.97536 16.57572 119.15384 2.0 0.0 0.0
> -1.0078617*
> *#@#  4  216  4.97536 16.37254 119.15384 2.0 0.0 0.0
> -1.0078768*
> *#@#  4  217  4.97536 14.89926 119.15384 2.0 0.0 0.0
> -1.0079292*
> *#@#  4  218  4.97536 14.85724 119.15384 2.0 0.0 0.0
> -1.0079303*
> *#@#  4  219  4.97536 12.95773 119.15384 2.0 0.0 0.0
> -1.0079467*
> *#@#  4  220  4.97536 13.40911 119.15384 2.0 0.0 0.0
> -1.0079498*
> *#@#  4  223  4.97536 13.62039 119.15384 2.0 0.0 0.0
> -1.0079516*
> *#@#  4  229  4.97536 13.61634 117.53580 2.0 0.0 0.0
> -1.0086172*
> *#@#  4  230  4.97536 13.61634 80.23408 2.0 0.0 0.0
> -1.0266197*
> *#@#  4  235  4.97536 13.61634 69.09492 2.0 0.0 0.0
> -1.0285894*
> *#@#  4  236  4.97536 13.61634 69.00322 2.0 0.0 0.0
> -1.0285913*
> *#@#  4  237  4.97536 13.

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

[Matthieu Vanhoutte]

Hi Douglas,

Dis you have time to take a look at ?

Best regards,
Matthieu

Le 3 oct. 2016 6:25 PM, "Matthieu Vanhoutte" 
a écrit :

> Hi Douglas,
>
> I have just sent it to you on Filedrop.
>
> Best regards,
> Matthieu
>
> 2016-10-03 17:45 GMT+02:00 Douglas Greve :
>
>> Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to
>> me on our filedrop?
>>
>> On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote:
>>
>> Hi Douglas,
>>
>> Please find below the mri_coreg terminal output :
>>
>> *$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $*
>> *cwd /NAS/tupac/matthieu/FS5.3/207118_M0_2014-01-29/pet*
>> *cmdline mri_coreg --s 207118_M0_2014-01-29 --mov BS7_PET.lps.nii.gz
>> --reg Pet2T1.BS7.register.dof6.mri_coreg.lta --regdat
>> Pet2T1.BS7.register.dof6.mri_coreg.dat *
>> *sysname  Linux*
>> *hostname yakuza*
>> *machine  x86_64*
>> *user matthieu*
>> *dof6*
>> *nsep2*
>> *cras01*
>> *ftol0.00*
>> *linmintol0.001000*
>> *bf   1*
>> *bflim30.00*
>> *bfnsamp30*
>> *SmoothRef 0*
>> *SatPct99.99*
>> *MovOOB 0*
>> *optschema 1*
>> *Reading in mov BS7_PET.lps.nii.gz*
>> *Reading in ref
>> /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/brainmask.mgz*
>> *Reading in and applying refmask
>> /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/aparc+aseg.mgz*
>> *Setting cras translation parameters to align centers*
>> *Creating random numbers for coordinate dithering*
>> *Performing intensity dithering*
>> *Initial parameters 20.9141 11.8161 149.1538  0.  0.  0.
>>  1.  1.  1.  0.  0.  0. *
>> *Separation list (2):  4  2   min = 2*
>> *DoSmoothing 1*
>> *DoCoordDither 1*
>> *DoIntensityDither 1*
>> *nitersmax 4*
>> *ftol 1.000e-07*
>> *linmintol 1.000e-03*
>> *SatPct 99.99*
>> *Hist FWHM 7.00 7.00*
>> *nthreads 1*
>> *movsat = 10897.7666*
>> *mov gstd 0.8459 0.8459 0.8459*
>> *Smoothing mov*
>> *refsat = 119.*
>> *ref gstd 0.8459 0.8459 0.8459*
>> *Smoothing ref*
>> *COREGpreproc() done*
>> *Testing if mov and target overlap*
>> *Init cost   -1.0011578057*
>> *nhits = 262144 out of 16777216, Percent Overlap: 100.0*
>> *Initial  RefRAS-to-MovRAS*
>> * 1.0   0.0   0.0   20.91408;*
>> * 0.0   1.0   0.0   11.81612;*
>> * 0.0   0.0   1.0   149.15384;*
>> * 0.0   0.0   0.0   1.0;*
>> *Initial  RefVox-to-MovVox*
>> * 1.0   0.0   0.0   0.0;*
>> * 0.0   0.0  -1.0   255.0;*
>> * 0.0  -1.0   0.0   255.0;*
>> * 0.0   0.0   0.0   1.0;*
>> *sep = 4 ---*
>> *COREGoptBruteForce() 30 1 30*
>> *Turning on MovOOB for BruteForce Search*
>> *#BF# sep= 4 iter=0 lim=30.0 delta=2.00   4.91408  21.81612 119.15384
>> 2.0   0.0   0.0   -1.0078773*
>> *Turning  MovOOB back off after brute force search*
>>
>>
>> *-*
>> *Init Powel Params dof = 6*
>> *Starting OpenPowel2(), sep = 4*
>> *InitialCost-1.0076701641 *
>> *#@#  4  188  4.91408 21.81612 119.15384 2.0 0.0 0.0
>> -1.0076702*
>> *fs_powell::minimize*
>> *  nparams 6*
>> *  maxfev 4*
>> *  ftol   0.00*
>> *  linmin_xtol_   0.001000*
>> *  powell nthiter 0: fret = -1.007670*
>> *#@#  4  197  4.93866 21.81612 119.15384 2.0 0.0 0.0
>> -1.0076704*
>> *#@#  4  198  4.96905 21.81612 119.15384 2.0 0.0 0.0
>> -1.0076705*
>> *#@#  4  209  4.97536 20.19808 119.15384 2.0 0.0 0.0
>> -1.0077189*
>> *#@#  4  210  4.97536 19.55424 119.15384 2.0 0.0 0.0
>> -1.0077529*
>> *#@#  4  211  4.97536 18.51247 119.15384 2.0 0.0 0.0
>> -1.0078081*
>> *#@#  4  212  4.97536 16.82685 119.15384 2.0 0.0 0.0
>> -1.0078434*
>> *#@#  4  213  4.97536 16.77889 119.15384 2.0 0.0 0.0
>> -1.0078460*
>> *#@#  4  214  4.97536 16.70129 119.15384 2.0 0.0 0.0
>> -1.0078515*
>> *#@#  4  215  4.97536 16.57572 119.15384 2.0 0.0 0.0
>> -1.0078617*
>> *#@#  4  216  4.97536 16.37254 119.15384 2.0 0.0 0.0
>> -1.0078768*
>> *#@#  4  217  4.97536 14.89926 119.15384 2.0 0.0 0.0
>> -1.0079292*
>> *#@#  4  218  4.97536 14.85724 119.15384 2.0 0.0 0.0
>> -1.007930

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

[Matthieu Vanhoutte]

Thank you for your diagnosis Douglas. How could I get the voxel sizes right
from input nifti pet and mri data ?

Best regards,
Matthieu

Le 12 oct. 2016 10:05 PM, "Douglas N Greve"  a
écrit :

> The problem appears to be that the PET or the MRI (or both) have
> incorrect voxel sizes (about 15%). You need to fix the problem. You can
> get a decent registration using something like
>
> mri_coreg --mov BS7_PET.lps.nii.gz --s 207118_FS_Filedrop --reg
> dof9.wb.lta --dof 9 --no-ref-mask --ref mri/orig.mgz
>
> with 9 DOF instead of 6 to account for the scaling (voxel size error).
> But it is *much* better to get the voxel sizes right and use 6 dof
>
>
> On 10/06/2016 02:50 PM, Matthieu Vanhoutte wrote:
> >
> > Hi Douglas,
> >
> > Dis you have time to take a look at ?
> >
> > Best regards,
> > Matthieu
> >
> >
> > Le 3 oct. 2016 6:25 PM, "Matthieu Vanhoutte"
> > mailto:matthieuvanhou...@gmail.com>> a
> > écrit :
> >
> > Hi Douglas,
> >
> > I have just sent it to you on Filedrop.
> >
> > Best regards,
> > Matthieu
> >
> > 2016-10-03 17:45 GMT+02:00 Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> > Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and
> > send it to me on our filedrop?
> >
> >
> > On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote:
> >> Hi Douglas,
> >>
> >> Please find below the mri_coreg terminal output :
> >> /
> >> /
> >> /$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $/
> >> /cwd /NAS/tupac/matthieu/FS5.3/207118_M0_2014-01-29/pet/
> >> /cmdline mri_coreg --s 207118_M0_2014-01-29 --mov
> >> BS7_PET.lps.nii.gz --reg
> >> Pet2T1.BS7.register.dof6.mri_coreg.lta --regdat
> >> Pet2T1.BS7.register.dof6.mri_coreg.dat /
> >> /sysname  Linux/
> >> /hostname yakuza/
> >> /machine  x86_64/
> >> /user matthieu/
> >> /dof6/
> >> /nsep2/
> >> /cras01/
> >> /ftol0.00/
> >> /linmintol0.001000/
> >> /bf   1/
> >> /bflim30.00/
> >> /bfnsamp30/
> >> /SmoothRef 0/
> >> /SatPct99.99/
> >> /MovOOB 0/
> >> /optschema 1/
> >> /Reading in mov BS7_PET.lps.nii.gz/
> >> /Reading in ref
> >> /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/
> brainmask.mgz/
> >> /Reading in and applying refmask
> >> /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/
> aparc+aseg.mgz/
> >> /Setting cras translation parameters to align centers/
> >> /Creating random numbers for coordinate dithering/
> >> /Performing intensity dithering/
> >> /Initial parameters 20.9141 11.8161 149.1538  0.  0.
> >>  0.  1.  1.  1.  0.  0.  0. /
> >> /Separation list (2):  4  2   min = 2/
> >> /DoSmoothing 1/
> >> /DoCoordDither 1/
> >> /DoIntensityDither 1/
> >> /nitersmax 4/
> >> /ftol 1.000e-07/
> >> /linmintol 1.000e-03/
> >> /SatPct 99.99/
> >> /Hist FWHM 7.00 7.00/
> >> /nthreads 1/
> >> /movsat = 10897.7666/
> >> /mov gstd 0.8459 0.8459 0.8459/
> >> /Smoothing mov/
> >> /refsat = 119./
> >> /ref gstd 0.8459 0.8459 0.8459/
> >> /Smoothing ref/
> >> /COREGpreproc() done/
> >> /Testing if mov and target overlap/
> >> /Init cost   -1.0011578057/
> >> /nhits = 262144 out of 16777216, Percent Overlap: 100.0/
> >> /Initial  RefRAS-to-MovRAS/
> >> / 1.0   0.0   0.0 20.91408;/
> >> / 0.0   1.0   0.0 11.81612;/
> >> / 0.0   0.0   1.0 149.15384;/
> >> / 0.0   0.0   0.0 1.0;/
> >> /Initial  RefVox-to-MovVox/
> >> / 1.0   0.0   0.0 0.0;/
> >> / 0.0   0.0  -1.0 255.0;/
> >> / 0.0  -1.0   0.0 255.0;/
> >> / 0.0   0.000

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Dear Freesurfer's experts,

Could anyone please explain me the difference I got with command line in
below mail ?

Best regards,
Matthieu

2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte :

> Dear experts,
>
> I am in trouble with two ways of computing mean intensity with
> mri_segstats.
>
> First I have used on .annot files with three different labels inside
> (SegId 1 to 3) :
>
> *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i
> lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum*
>
> which give me those results:
> # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
> Max Range
>   1   1 2780514182.6  cluster-0018.8194
>   1.4351 6.210514.2947 8.0842
>   2   2  2321 1047.3  cluster-002   10.3661
>   1.0848 8.837512.9317 4.0942
>   3   3   552  313.1  cluster3  10.3365
>   0.4711 9.371911.8694 2.4975
>
> Second I have created on .label files containing the three segmented
> labels (SegId 1 to 3) and used this label with mri_segstats:
>
> *mri_segstats --slabel fsaverage lh lh.th23.cluster.thresh1.3.label --i
> lh.PET.fsaverage.sm10.mgh --excludeid 0 --sum lh.pet.label.sum *
>
> which give me those results:
> *# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
> Max Range  *
> *  1   1 3067815542.9  Seg0001 8.9637 1.4701 6.2105
>  14.2947 8.0842 *
>
> I verified if I obtained the same results with the two ways (.annot or
> .label) and everything is fine comparing NVertices, Area_mm2 but Mean in
> first way gives me (8.8194+10.3661+10.3365)/3 = 9.84066 and with .label
> file Mean = 8.9637.
>
> Did I have miss anything and how is computed mean intensity ?
>
> Many thanks in advance.
>
> Best regards,
> Matthieu
>
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Thank you Douglas !

Le 10 nov. 2016 7:21 PM, "Douglas N Greve"  a
écrit :

> You need to weight by the number of vertices
>
> n = [27805 2321 552];
>   m = [8.8194 10.3661 10.3365];
> sum(n.*m)/sum(n)
>
> ans =
>
>  8.9637
>
>
> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
> > Dear Freesurfer's experts,
> >
> > Could anyone please explain me the difference I got with command line
> > in below mail ?
> >
> > Best regards,
> > Matthieu
> >
> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte
> > mailto:matthieuvanhou...@gmail.com>>:
> >
> > Dear experts,
> >
> > I am in trouble with two ways of computing mean intensity with
> > mri_segstats.
> >
> > First I have used on .annot files with three different labels
> > inside (SegId 1 to 3) :
> >
> > /mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot
> > --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum/
> > /
> > /
> > which give me those results:
> > # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> > StdDev Min Max Range
> > 1   1 2780514182.6  cluster-001  8.8194 1.4351
> > 6.210514.2947 8.0842
> > 2   2  2321 1047.3  cluster-002 10.3661 1.0848
> > 8.837512.9317 4.0942
> > 3   3   552  313.1  cluster3  10.3365 0.4711
> > 9.371911.8694 2.4975
> >
> > Second I have created on .label files containing the three
> > segmented labels (SegId 1 to 3) and used this label with
> mri_segstats:
> >
> > /mri_segstats --slabel fsaverage lh
> > lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh
> > --excludeid 0 --sum lh.pet.label.sum /
> > /
> > /
> > which give me those results:/
> > /
> > /# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> > StdDev Min Max Range /
> > /  1   1 30678  15542.9  Seg0001 8.9637 1.4701 6.2105
> >  14.2947 8.0842 /
> > /
> > /
> > I verified if I obtained the same results with the two ways
> > (.annot or .label) and everything is fine comparing NVertices,
> > Area_mm2 but Mean in first way gives me (8.8194+10.3661+10.3365)/3
> > = 9.84066 and with .label file Mean = 8.9637.
> >
> > Did I have miss anything and how is computed mean intensity ?
> >
> > Many thanks in advance.
> >
> > Best regards,
> > Matthieu
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Dear Douglas,

I come back to you concerning stats made from binary .mgh surface data file:

mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh --excludeid 
0 --sum lh.bin.sum --avgwf lh.wav.bin.txt 

In the output file « lh.bin.sum » all is considered as volume input/output as 
you could see below:

# InVolFileTimeStamp  2016/04/28 09:46:19 
# InVolFrame 0 
# ExcludeSegId 0 
# Only reporting non-empty segmentations
# VoxelVolume_mm3 1 
# TableCol  1 ColHeader Index 
# TableCol  1 FieldName Index 
# TableCol  1 Units NA 
# TableCol  2 ColHeader SegId 
# TableCol  2 FieldName Segmentation Id
# TableCol  2 Units NA
# TableCol  3 ColHeader NVoxels 
# TableCol  3 FieldName Number of Voxels
# TableCol  3 Units unitless
# TableCol  4 ColHeader Volume_mm3
# TableCol  4 FieldName Volume
# TableCol  4 Units mm^3
# TableCol  5 ColHeader Mean 
# TableCol  5 FieldName Intensity Mean
# TableCol  5 Units unknown
# TableCol  6 ColHeader StdDev
# TableCol  6 FieldName Itensity StdDev
# TableCol  6 Units unknown
# TableCol  7 ColHeader Min
# TableCol  7 FieldName Intensity Min
# TableCol  7 Units unknown
# TableCol  8 ColHeader Max
# TableCol  8 FieldName Intensity Max
# TableCol  8 Units unknown
# TableCol  9 ColHeader Range
# TableCol  9 FieldName Intensity Range
# TableCol  9 Units unknown
# NRows 1 
# NTableCols 9 
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max 
Range  
  1   1 1151011510.0  Seg0001 7.6819 1.4396 4.4862
10.9042 6.4180 

As my inputs are all surface data could I consider that NVoxels is equal to 
NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ?

Best regards,
Matthieu

> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte  a 
> écrit :
> 
> Thank you Douglas !
> 
> 
> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"  <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
> You need to weight by the number of vertices
> 
> n = [27805 2321 552];
>   m = [8.8194 10.3661 10.3365];
> sum(n.*m)/sum(n)
> 
> ans =
> 
>  8.9637
> 
> 
> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
> > Dear Freesurfer's experts,
> >
> > Could anyone please explain me the difference I got with command line
> > in below mail ?
> >
> > Best regards,
> > Matthieu
> >
> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte
> > mailto:matthieuvanhou...@gmail.com> 
> > <mailto:matthieuvanhou...@gmail.com <mailto:matthieuvanhou...@gmail.com>>>:
> >
> > Dear experts,
> >
> > I am in trouble with two ways of computing mean intensity with
> > mri_segstats.
> >
> > First I have used on .annot files with three different labels
> > inside (SegId 1 to 3) :
> >
> > /mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot
> > --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum/
> > /
> > /
> > which give me those results:
> > # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> > StdDev Min Max Range
> > 1   1 2780514182.6  cluster-001  8.8194 1.4351
> > 6.210514.2947 8.0842
> > 2   2  2321 1047.3  cluster-002 10.3661 1.0848
> > 8.837512.9317 4.0942
> > 3   3   552  313.1  cluster3  10.3365 0.4711
> > 9.371911.8694 2.4975
> >
> > Second I have created on .label files containing the three
> > segmented labels (SegId 1 to 3) and used this label with mri_segstats:
> >
> > /mri_segstats --slabel fsaverage lh
> > lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh
> > --excludeid 0 --sum lh.pet.label.sum /
> > /
> > /
> > which give me those results:/
> > /
> > /# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> > StdDev Min Max Range /
> > /  1   1 30678  15542.9  Seg0001 8.9637 1.4701 6.2105
> >  14.2947 8.0842 /
> > /
> > /
> > I verified if I obtained the same results with the two ways
> > (.annot or .label) and everything is fine comparing NVertices,
> > Area_mm2 but Mean in first way gives me (8.8194+10.3661+10.3365)/3
> > = 9.84066 and with .label file Mean = 8.9637.
> >
> > Did I have miss anything and how is computed mean intensity ?
> >
> > Many thanks in advance.
> >
> > Best regards,
> > Matthieu
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Dear Douglas,

Yes I would like to in order to compute mean of some means. Maybe not if it
is equivalent to number of vertices (are vertices distributed equaly
distant on the cortical surface ?)

In case I need surface area, do I have to convert overlay to annotation
file to be used with mri_segstats ?

Best regards,
Matthieu

Le 11 nov. 2016 9:21 PM, "Douglas N Greve"  a
écrit :

> NVox is the number of vertices. The Volume_mm3 is not meaningful. Do you
> want area?
>
>
> On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > I come back to you concerning stats made from binary .mgh surface data
> > file:
> >
> > mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh
> > --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt
> >
> > In the output file « lh.bin.sum » all is considered as volume
> > input/output as you could see below:
> >
> > /# InVolFileTimeStamp  2016/04/28 09:46:19 /
> > /# InVolFrame 0 /
> > /# ExcludeSegId 0 /
> > /# Only reporting non-empty segmentations/
> > /# VoxelVolume_mm3 1 /
> > /# TableCol  1 ColHeader Index /
> > /# TableCol  1 FieldName Index /
> > /# TableCol  1 Units NA /
> > /# TableCol  2 ColHeader SegId /
> > /# TableCol  2 FieldName Segmentation Id/
> > /# TableCol  2 Units NA/
> > /# TableCol  3 ColHeader NVoxels /
> > /# TableCol  3 FieldName Number of Voxels/
> > /# TableCol  3 Units unitless/
> > /# TableCol  4 ColHeader Volume_mm3/
> > /# TableCol  4 FieldName Volume/
> > /# TableCol  4 Units mm^3/
> > /# TableCol  5 ColHeader Mean /
> > /# TableCol  5 FieldName Intensity Mean/
> > /# TableCol  5 Units unknown/
> > /# TableCol  6 ColHeader StdDev/
> > /# TableCol  6 FieldName Itensity StdDev/
> > /# TableCol  6 Units unknown/
> > /# TableCol  7 ColHeader Min/
> > /# TableCol  7 FieldName Intensity Min/
> > /# TableCol  7 Units unknown/
> > /# TableCol  8 ColHeader Max/
> > /# TableCol  8 FieldName Intensity Max/
> > /# TableCol  8 Units unknown/
> > /# TableCol  9 ColHeader Range/
> > /# TableCol  9 FieldName Intensity Range/
> > /# TableCol  9 Units unknown/
> > /# NRows 1 /
> > /# NTableCols 9 /
> > /# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev
> > Min Max Range /
> > /  1   1 1151011510.0  Seg0001 7.6819 1.4396
> > 4.486210.9042 6.4180 /
> >
> > As my inputs are all surface data could I consider that NVoxels is
> > equal to NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ?
> >
> > Best regards,
> > Matthieu
> >
> >> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte
> >> mailto:matthieuvanhou...@gmail.com>> a
> >> écrit :
> >>
> >> Thank you Douglas !
> >>
> >>
> >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"  >> <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
> >>
> >> You need to weight by the number of vertices
> >>
> >> n = [27805 2321 552];
> >>   m = [8.8194 10.3661 10.3365];
> >> sum(n.*m)/sum(n)
> >>
> >> ans =
> >>
> >>  8.9637
> >>
> >>
> >> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
> >> > Dear Freesurfer's experts,
> >> >
> >> > Could anyone please explain me the difference I got with
> >> command line
> >> > in below mail ?
> >> >
> >> > Best regards,
> >> > Matthieu
> >> >
> >> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte
> >> >  >> <mailto:matthieuvanhou...@gmail.com>
> >> <mailto:matthieuvanhou...@gmail.com
> >> <mailto:matthieuvanhou...@gmail.com>>>:
> >> >
> >> > Dear experts,
> >> >
> >> > I am in trouble with two ways of computing mean intensity with
> >> > mri_segstats.
> >> >
> >> > First I have used on .annot files with three different labels
> >> > inside (SegId 1 to 3) :
> >> >
> >> > /mri_segstats --annot fsaverage lh
> cache.th23.pos.sig.ocn.annot
> >> > --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum/
> >> > /
> >> > /
> >> > which give me those results:
> >> > # ColHeaders  Index SegId NVertice

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Thank you Douglas for giving me a way to compute area from segmented
surface data.

Are vertices equally spaced along cortex or do triangles all have same area
?

Best,
Matthieu

Le 11 nov. 2016 10:55 PM, "Douglas N Greve"  a
écrit :

If you want to do it on fsaverage, then

mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh --seg
lh.sign_clust.bin.mgh
--excludeid 0 --sum lh.bin.area.sum --accumulate




On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote:
>
> Dear Douglas,
>
> Yes I would like to in order to compute mean of some means. Maybe not
> if it is equivalent to number of vertices (are vertices distributed
> equaly distant on the cortical surface ?)
>
> In case I need surface area, do I have to convert overlay to
> annotation file to be used with mri_segstats ?
>
> Best regards,
> Matthieu
>
>
> Le 11 nov. 2016 9:21 PM, "Douglas N Greve"  <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
>
> NVox is the number of vertices. The Volume_mm3 is not meaningful.
> Do you
> want area?
>
>
> On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > I come back to you concerning stats made from binary .mgh
> surface data
> > file:
> >
> > mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh
> > --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt
> >
> > In the output file « lh.bin.sum » all is considered as volume
> > input/output as you could see below:
> >
> > /# InVolFileTimeStamp  2016/04/28 09:46:19 /
> > /# InVolFrame 0 /
> > /# ExcludeSegId 0 /
> > /# Only reporting non-empty segmentations/
> > /# VoxelVolume_mm3 1 /
> > /# TableCol  1 ColHeader Index /
> > /# TableCol  1 FieldName Index /
> > /# TableCol  1 Units NA /
> > /# TableCol  2 ColHeader SegId /
> > /# TableCol  2 FieldName Segmentation Id/
> > /# TableCol  2 Units NA/
> > /# TableCol  3 ColHeader NVoxels /
> > /# TableCol  3 FieldName Number of Voxels/
> > /# TableCol  3 Units unitless/
> > /# TableCol  4 ColHeader Volume_mm3/
> > /# TableCol  4 FieldName Volume/
> > /# TableCol  4 Units mm^3/
> > /# TableCol  5 ColHeader Mean /
> > /# TableCol  5 FieldName Intensity Mean/
> > /# TableCol  5 Units unknown/
> > /# TableCol  6 ColHeader StdDev/
> > /# TableCol  6 FieldName Itensity StdDev/
> > /# TableCol  6 Units unknown/
> > /# TableCol  7 ColHeader Min/
> > /# TableCol  7 FieldName Intensity Min/
> > /# TableCol  7 Units unknown/
> > /# TableCol  8 ColHeader Max/
> > /# TableCol  8 FieldName Intensity Max/
> > /# TableCol  8 Units unknown/
> > /# TableCol  9 ColHeader Range/
> > /# TableCol  9 FieldName Intensity Range/
> > /# TableCol  9 Units unknown/
> > /# NRows 1 /
> > /# NTableCols 9 /
> > /# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev
>     > Min Max Range /
> > /  1   1 1151011510.0  Seg0001 7.6819  1.4396
> > 4.486210.9042 6.4180 /
> >
> > As my inputs are all surface data could I consider that NVoxels is
> > equal to NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ?
> >
> > Best regards,
> > Matthieu
> >
> >> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte
> >>  <mailto:matthieuvanhou...@gmail.com>
> <mailto:matthieuvanhou...@gmail.com
> <mailto:matthieuvanhou...@gmail.com>>> a
> >> écrit :
> >>
> >> Thank you Douglas !
> >>
> >>
> >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"
> mailto:gr...@nmr.mgh.harvard.edu>
> >> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>> a écrit :
> >>
> >> You need to weight by the number of vertices
> >>
> >> n = [27805 2321 552];
> >>   m = [8.8194 10.3661 10.3365];
> >> sum(n.*m)/sum(n)
> >>
> >> ans =
> >>
> >>  8.9637
> >>
> >>
> >> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
> >> > Dear Freesurfer's experts,
> >> >
> >> > Could anyone please explain me the difference I got with
> >> command line
> >&g

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Is it better to compute mean to weight by number of vertices or surface
area ?

Best,
Matthieu

Le 11 nov. 2016 11:33 PM, "Douglas N Greve"  a
écrit :

> Vertices do not have equal areas and are not equally spaced
>
>
> On 11/11/2016 05:11 PM, Matthieu Vanhoutte wrote:
> >
> > Thank you Douglas for giving me a way to compute area from segmented
> > surface data.
> >
> > Are vertices equally spaced along cortex or do triangles all have same
> > area ?
> >
> > Best,
> > Matthieu
> >
> >
> > Le 11 nov. 2016 10:55 PM, "Douglas N Greve"  > <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
> >
> > If you want to do it on fsaverage, then
> >
> > mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh
> --seg
> > lh.sign_clust.bin.mgh
> > --excludeid 0 --sum lh.bin.area.sum --accumulate
> >
> >
> >
> >
> > On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote:
> > >
> > > Dear Douglas,
> > >
> > > Yes I would like to in order to compute mean of some means.
> > Maybe not
> > > if it is equivalent to number of vertices (are vertices distributed
> > > equaly distant on the cortical surface ?)
> > >
> > > In case I need surface area, do I have to convert overlay to
> > > annotation file to be used with mri_segstats ?
> > >
> > > Best regards,
> > > Matthieu
> > >
> > >
> > > Le 11 nov. 2016 9:21 PM, "Douglas N Greve"
> > mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> a écrit :
> > >
> > > NVox is the number of vertices. The Volume_mm3 is not
> > meaningful.
> > > Do you
> > > want area?
> > >
> > >
> > > On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote:
> > > > Dear Douglas,
> > > >
> > > > I come back to you concerning stats made from binary .mgh
> > > surface data
> > > > file:
> > > >
> > > > mri_segstats --i lh.fsaverage.sm10.mgh --seg
> > lh.sign_clust.bin.mgh
> > > > --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt
> > > >
> > > > In the output file « lh.bin.sum » all is considered as volume
> > > > input/output as you could see below:
> > > >
> > > > /# InVolFileTimeStamp  2016/04/28 09:46:19 /
> > > > /# InVolFrame 0 /
> > > > /# ExcludeSegId 0 /
> > > > /# Only reporting non-empty segmentations/
> > > > /# VoxelVolume_mm3 1 /
> > > > /# TableCol  1 ColHeader Index /
> > > > /# TableCol  1 FieldName Index /
> > > > /# TableCol  1 Units NA /
> > > > /# TableCol  2 ColHeader SegId /
> > > > /# TableCol  2 FieldName Segmentation Id/
> > > > /# TableCol  2 Units NA/
> > > > /# TableCol  3 ColHeader NVoxels /
> > > > /# TableCol  3 FieldName Number of Voxels/
> > > > /# TableCol  3 Units unitless/
> > > > /# TableCol  4 ColHeader Volume_mm3/
> > > > /# TableCol  4 FieldName Volume/
> > > > /# TableCol  4 Units mm^3/
> > > > /# TableCol  5 ColHeader Mean /
> > > > /# TableCol  5 FieldName Intensity Mean/
> > > > /# TableCol  5 Units unknown/
> > > > /# TableCol  6 ColHeader StdDev/
> > > > /# TableCol  6 FieldName Itensity StdDev/
> > > > /# TableCol  6 Units unknown/
> > > > /# TableCol  7 ColHeader Min/
> > > > /# TableCol  7 FieldName Intensity Min/
> > > > /# TableCol  7 Units unknown/
> > > > /# TableCol  8 ColHeader Max/
> > > > /# TableCol  8 FieldName Intensity Max/
> > > > /# TableCol  8 Units unknown/
> > > > /# TableCol  9 ColHeader Range/
> > > > /# TableCol  9 FieldName Intensity Range/
> > > > /# TableCol  9 Units unknown/
> > > > /# NRows 1 /
> > > > /# NTableCols 9 /
> > &

Re: [Freesurfer] Longitudinal surface analysis of PET data

[Matthieu Vanhoutte]

Dear Freesurfer's experts,

I come back to you concerning questions of registrations.

Since during the longitudinal process each --long subject directory has
been registered onto the common --base template, shouldn't I:

1) Register PET data onto the subject cross-sectional directory (native
data) with rigid-body transformation
2) Then take into account the registration between --cross and --long
directory subject and apply the registration to the PET first registered
onto native space ? In this case, how and where is this transformation has
been saved ?

Best regards,
Matthieu

2016-09-30 23:05 GMT+02:00 Douglas N Greve :

> Yes
>
>
> On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote:
> >
> > Hi Douglas,
> >
> > Does the surface of the closest MRI time point mean the surface of the
> > -long subject time point directory rather than cross-sectional subject
> > time point directory ?
> >
> > Best regards,
> > Matthieu
> >
> >
> > Le 30 sept. 2016 9:14 PM, "Douglas N Greve"  > <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
> >
> > There is no such long process for PET. The idea is that you
> > process the
> > MRI in a longitudinal way, then sample the PET data onto the
> > surface of
> >     the closest MRI time point. Then proceed in a way similar to the
> > thickness analysis
> >
> >
> > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote:
> > > Dear Freesurfer's experts,
> > >
> > > Could you answer me about my last question with no response in the
> > > mail below ?
> > >
> > > When using cortical thickness in longitudinal analysis with LME, we
> > > used lh.thickness or rh.thickness from -long subject directories.
> > > These data followed particular processing steps including
> > > registrations in order to use them with more precision in
> > longitudinal
> > > studies, didn't they ?
> > >
> > > My problem is that I would like to perform longitudinal study on
> PET
> > > data images with LME. So I wonder if I just have to resample onto
> > > -long cortical subject surface ? Do I need to follow the same steps
> > > than cortical thickness from cross-sectional to -long subject
> > > directories ? If this is the case, which commands should I use to
> > > mimic cortical thickness longitudinal data ?
> > >
> > > Many thanks in advance for helping !
> > >
> > > Best regards,
> > > Matthieu
> > >
> > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte
> > >  > <mailto:matthieuvanhou...@gmail.com>
> > <mailto:matthieuvanhou...@gmail.com
> > <mailto:matthieuvanhou...@gmail.com>>>:
> > >
> > > Hi Martin,
> > >
> > > Thanks for your answer. However, it seems to me that cortical
> > > thickness follow a particular process with the recon-all -long
> > > process, isn’t it ? Is there any resample onto average time
> > > subject then other operation following ?
> > >
> > > Best regards,
> > > Matthieu
> > >
> > > > Le 18 sept. 2016 à 16:26, Martin Reuter
> > >  > <mailto:mreu...@nmr.mgh.harvard.edu>
> > <mailto:mreu...@nmr.mgh.harvard.edu
> > <mailto:mreu...@nmr.mgh.harvard.edu>>>
> > > a écrit :
> > > >
> > > > Hi Matthieu,
> > > >
> > > > I never used PET data, but once you manage to resample you
> pet
> > > data onto the surface, you will have a file similar to the
> > > thickness file for each subjects. Instead of thickness it holds
> > > you PET information. From that point on everything should be
> > > identical to the thickness analysis.
> > > >
> > > > So this is really more a question how to get your PET data
> > > sampled onto the surface. If no one else replies, write that
> > into
> > > the subject line and repost.
> > > >
> > > > Best, Martin
> > > >
> > > >
> > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte
> > >  > <mailto:matthieuv

Re: [Freesurfer] Longitudinal surface analysis of PET data

[Matthieu Vanhoutte]

Still using rigid-body registration on --long subject directory ?

 Or is affine registration in this case needed ?

Best regards,
Matthieu

2016-11-14 17:12 GMT+01:00 Douglas N Greve :

> I would just register the pet to the closest (in time) anatomical
>
>
> On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote:
> > Dear Freesurfer's experts,
> >
> > I come back to you concerning questions of registrations.
> >
> > Since during the longitudinal process each --long subject directory
> > has been registered onto the common --base template, shouldn't I:
> >
> > 1) Register PET data onto the subject cross-sectional directory
> > (native data) with rigid-body transformation
> > 2) Then take into account the registration between --cross and --long
> > directory subject and apply the registration to the PET first
> > registered onto native space ? In this case, how and where is this
> > transformation has been saved ?
> >
> > Best regards,
> > Matthieu
> >
> > 2016-09-30 23:05 GMT+02:00 Douglas N Greve  > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> > Yes
> >
> >
> > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote:
> > >
> > > Hi Douglas,
> > >
> > > Does the surface of the closest MRI time point mean the surface
> > of the
> > > -long subject time point directory rather than cross-sectional
> > subject
> > > time point directory ?
> > >
> > > Best regards,
> > > Matthieu
> > >
> > >
> > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve"
> > mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> a écrit :
> > >
> > > There is no such long process for PET. The idea is that you
> > > process the
> > > MRI in a longitudinal way, then sample the PET data onto the
> > > surface of
> > > the closest MRI time point. Then proceed in a way similar to
> the
> > > thickness analysis
> > >
> > >
> > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote:
> > > > Dear Freesurfer's experts,
> > > >
> > > > Could you answer me about my last question with no
> > response in the
> > > > mail below ?
> > > >
> > > > When using cortical thickness in longitudinal analysis
> > with LME, we
> > > > used lh.thickness or rh.thickness from -long subject
> > directories.
> > > > These data followed particular processing steps including
> > > > registrations in order to use them with more precision in
> > > longitudinal
> > > > studies, didn't they ?
> > > >
> > > > My problem is that I would like to perform longitudinal
> > study on PET
> > > > data images with LME. So I wonder if I just have to
> > resample onto
> > > > -long cortical subject surface ? Do I need to follow the
> > same steps
> > > > than cortical thickness from cross-sectional to -long subject
> > > > directories ? If this is the case, which commands should I
> > use to
> > > > mimic cortical thickness longitudinal data ?
> > > >
> > > > Many thanks in advance for helping !
> > > >
> > > > Best regards,
> > > > Matthieu
> > > >
> > > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte
> > > >  > <mailto:matthieuvanhou...@gmail.com>
> > > <mailto:matthieuvanhou...@gmail.com
> > <mailto:matthieuvanhou...@gmail.com>>
> > > <mailto:matthieuvanhou...@gmail.com
> > <mailto:matthieuvanhou...@gmail.com>
> > > <mailto:matthieuvanhou...@gmail.com <mailto:matthieuvanhoutte@
> gmail.com>>>>:
> > > >
> > > > Hi Martin,
> > > >
> > > > Thanks for your answer. However, it seems to me that
> > cortical
> > > > thickness follow a particular process with the
> > recon-all -long
> > > > process, isn’t it ? Is

Re: [Freesurfer] Longitudinal surface analysis of PET data

[Matthieu Vanhoutte]

Thank you !

Best regards,
Matthieu

2016-11-14 17:48 GMT+01:00 Douglas N Greve :

> Rigid.
>
>
> On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote:
> > Still using rigid-body registration on --long subject directory ?
> >
> >  Or is affine registration in this case needed ?
> >
> > Best regards,
> > Matthieu
> >
> > 2016-11-14 17:12 GMT+01:00 Douglas N Greve  > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> > I would just register the pet to the closest (in time) anatomical
> >
> >
> > On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote:
> > > Dear Freesurfer's experts,
> > >
> > > I come back to you concerning questions of registrations.
> > >
> > > Since during the longitudinal process each --long subject directory
> > > has been registered onto the common --base template, shouldn't I:
> > >
> > > 1) Register PET data onto the subject cross-sectional directory
> > > (native data) with rigid-body transformation
> > > 2) Then take into account the registration between --cross and
> > --long
> > > directory subject and apply the registration to the PET first
> > > registered onto native space ? In this case, how and where is this
> > > transformation has been saved ?
> > >
> > > Best regards,
> > > Matthieu
> > >
> > > 2016-09-30 23:05 GMT+02:00 Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>>:
> > >
> > > Yes
> > >
> > >
> > > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote:
> > > >
> > > > Hi Douglas,
> > > >
> > > > Does the surface of the closest MRI time point mean the
> > surface
> > > of the
> > > > -long subject time point directory rather than
> cross-sectional
> > > subject
> > > > time point directory ?
> > > >
> > > > Best regards,
> > > > Matthieu
> > > >
> > > >
> > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve"
> > >  > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
> >>
> > > > <mailto:gr...@nmr.mgh.harvard.edu
> >     <mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>>> a écrit :
> > > >
> > > > There is no such long process for PET. The idea is
> > that you
> > > > process the
> > > > MRI in a longitudinal way, then sample the PET data
> > onto the
> > > > surface of
> > > > the closest MRI time point. Then proceed in a way
> > similar to the
> > > > thickness analysis
> > > >
> > > >
> > > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote:
> > > > > Dear Freesurfer's experts,
> > > > >
> > > > > Could you answer me about my last question with no
> > > response in the
> > > > > mail below ?
> > > > >
> > > > > When using cortical thickness in longitudinal analysis
> > > with LME, we
> > > > > used lh.thickness or rh.thickness from -long subject
> > > directories.
> > > > > These data followed particular processing steps
> > including
> > > > > registrations in order to use them with more
> > precision in
> > > > longitudinal
> > > > > studies, didn't they ?
> > > > >
> > > > > My problem is that I would like to perform longitudinal
> > > study on PET
> > > > > data images with LME. So I wonder if I just have to
> > > resample onto
> > > > > -long cortical subject surface ? Do I need to follow
> the
> > >   

Re: [Freesurfer] Longitudinal surface analysis of PET data

[Matthieu Vanhoutte]

Hi Martin,

Thank you for clarifications !

1) What do you mean by "If, for some reason, the pet and MR (cross) are
already very close in space" ?

2) How could it be possible to directly register to the long time point ?
Since I use a rigid registration, the long time point T1 will not have been
deformed (affine or non linear) ?

Best regards,
Matthieu

2016-11-18 11:18 GMT+01:00 Martin Reuter :

> Hi Matthieu,
>
> to clarify, you can directly register to the long time point.
>
> If, for some reason, the pet and MR (cross) are already very close in
> space, it may make sense to first register to that, then concatenate that
> transform with the one from cross to long and then map the PET there. Don’t
> map it twice, instead concatenate the transforms.
> mri_concatenate_lta will do that.
>
> You find the transforms from base to each time point in the long
> mri/transforms directory and probably also in the base/mri/transforms dir.
>
> Best, Martin
>
> On Nov 14, 2016, at 5:49 PM, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> wrote:
>
> Thank you !
>
> Best regards,
> Matthieu
>
> 2016-11-14 17:48 GMT+01:00 Douglas N Greve :
>
>> Rigid.
>>
>>
>> On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote:
>> > Still using rigid-body registration on --long subject directory ?
>> >
>> >  Or is affine registration in this case needed ?
>> >
>> > Best regards,
>> > Matthieu
>> >
>> > 2016-11-14 17:12 GMT+01:00 Douglas N Greve > > <mailto:gr...@nmr.mgh.harvard.edu>>:
>> >
>> > I would just register the pet to the closest (in time) anatomical
>> >
>> >
>> > On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote:
>> > > Dear Freesurfer's experts,
>> > >
>> > > I come back to you concerning questions of registrations.
>> > >
>> > > Since during the longitudinal process each --long subject
>> directory
>> > > has been registered onto the common --base template, shouldn't I:
>> > >
>> > > 1) Register PET data onto the subject cross-sectional directory
>> > > (native data) with rigid-body transformation
>> > > 2) Then take into account the registration between --cross and
>> > --long
>> > > directory subject and apply the registration to the PET first
>> > > registered onto native space ? In this case, how and where is this
>> > > transformation has been saved ?
>> > >
>> > > Best regards,
>> > > Matthieu
>> > >
>> > > 2016-09-30 23:05 GMT+02:00 Douglas N Greve
>> > mailto:gr...@nmr.mgh.harvard.edu>
>> > > <mailto:gr...@nmr.mgh.harvard.edu
>> > <mailto:gr...@nmr.mgh.harvard.edu>>>:
>> > >
>> > > Yes
>> > >
>> > >
>> > > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote:
>> > > >
>> > > > Hi Douglas,
>> > > >
>> > > > Does the surface of the closest MRI time point mean the
>> > surface
>> > > of the
>> > > > -long subject time point directory rather than
>> cross-sectional
>> > > subject
>> > > > time point directory ?
>> > > >
>> > > > Best regards,
>> > > > Matthieu
>> > > >
>> > > >
>> > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve"
>> > > > > <mailto:gr...@nmr.mgh.harvard.edu>
>> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
>> >>
>> > > > <mailto:gr...@nmr.mgh.harvard.edu
>> > <mailto:gr...@nmr.mgh.harvard.edu>
>> > > <mailto:gr...@nmr.mgh.harvard.edu
>> > <mailto:gr...@nmr.mgh.harvard.edu>>>> a écrit :
>> > > >
>> > > > There is no such long process for PET. The idea is
>> > that you
>> > > > process the
>> > > > MRI in a longitudinal way, then sample the PET data
>> > onto the
>> > > > surface of
>> > > > the closest MRI time point. Then proceed in a way
>> > similar to the
>> > > 

[Freesurfer] Longitudinal stream : LME and limits of model

[Matthieu Vanhoutte]

Dear Freesurfer’s experts,

I would have some questions regarding the LME model to be used in longitudinal 
stream:

1) Which are the ratio limits or % of missing timepoints accepted ? (according 
time, I have less and less subjects time points)

2) Is it possible to include patients that would miss the first timepoint but 
got the others ?

3) Considering a group in longitudinal study, which is the number of subjects 
minimal of this group accepted for LME modeling ?

4) Finally, concerning quality control and among a big number of total time 
points, which essential controls are necessary ? (Control of norm.mgz of the 
base, alignment of longitudinal timepoints on base,… ?)

Best regards,
Matthieu


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Re: [Freesurfer] Longitudinal stream : LME and limits of model

[Matthieu Vanhoutte]

Hi Martin,

Thanks for replying. Please see inline below:

> Le 21 nov. 2016 à 20:26, Martin Reuter  a écrit :
> 
> Hi Matthieu, 
> 
> a few quick answers. Maybe Jorge knows more. 
> Generally number of subjects / time points etc. cannot be specified 
> generally. All depends on how noisy your data is and how large the effect is 
> that you expect to detect. You can do a power analysis in order to figure out 
> how many subject / time points would be needed. There are some tools for that 
> in the LME toolbox:
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#Poweranalysis
>  
> <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#Poweranalysis>
>  
> 
> 1. see above
> 2. yes, also time points can miss from the middle. If you have mainly missing 
> time points at the end, this will bias your analysis to some extend, as the 
> remaining ones may be extremely healthy, as probably the more diseased ones 
> drop out. You may want to do a time-to-event (or survival-analysis) which 
> considers early drop-out.

Is there any way to do with Freesurfer this kind of analysis ?

> 3. see above (power analysis)
> 4. GIGO means garbage in, garbage out, so the less you QC, the more likely 
> will your results be junk. The more you QC the less likely will it be junk, 
> but could still be. The FS wiki has lots of tutorial information on checking 
> freesurfer recons. For longitudinal, you should additionally check the 
> surfaces in the base, the brain mask in the base, and the alignment of the 
> time points (although there is some wiggle space for the alignment, as most 
> things are allowed to evolve further for each time point). 

For the alignment of the time points, should I better comparing brainmask or 
norm.mgz ?

In order to avoid bias by adding further time points in the model by the -add 
recon all command, is this better for each subject to take into account all the 
time points existing for it or only the ones that I will include in the model 
(three time points / subject ; if existing 6 time points for any subject ?)

Best regards,
Matthieu

> 
> Best, Martin
> 
>> On Nov 21, 2016, at 7:07 PM, Matthieu Vanhoutte > <mailto:matthieuvanhou...@gmail.com>> wrote:
>> 
>> Dear Freesurfer’s experts,
>> 
>> I would have some questions regarding the LME model to be used in 
>> longitudinal stream:
>> 
>> 1) Which are the ratio limits or % of missing timepoints accepted ? 
>> (according time, I have less and less subjects time points)
>> 
>> 2) Is it possible to include patients that would miss the first timepoint 
>> but got the others ?
>> 
>> 3) Considering a group in longitudinal study, which is the number of 
>> subjects minimal of this group accepted for LME modeling ?
>> 
>> 4) Finally, concerning quality control and among a big number of total time 
>> points, which essential controls are necessary ? (Control of norm.mgz of the 
>> base, alignment of longitudinal timepoints on base,… ?)
>> 
>> Best regards,
>> Matthieu
>> 
>> 
>> ___
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>> 
>> 
> 
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.

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Re: [Freesurfer] Longitudinal stream : LME and limits of model

[Matthieu Vanhoutte]

Hi Martin,

Please see inline below:

> Le 22 nov. 2016 à 17:04, Martin Reuter  a écrit :
> 
> Hi Matthieu, 
> (also inline)
> 
>> On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte 
>> mailto:matthieuvanhou...@gmail.com>> wrote:
>> 
>> Hi Martin,
>> 
>> Thanks for replying. Please see inline below:
>> 
>>> Le 21 nov. 2016 à 20:26, Martin Reuter >> <mailto:mreu...@nmr.mgh.harvard.edu>> a écrit :
>>> 
>>> Hi Matthieu, 
>>> 
>>> a few quick answers. Maybe Jorge knows more. 
>>> Generally number of subjects / time points etc. cannot be specified 
>>> generally. All depends on how noisy your data is and how large the effect 
>>> is that you expect to detect. You can do a power analysis in order to 
>>> figure out how many subject / time points would be needed. There are some 
>>> tools for that in the LME toolbox:
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#Poweranalysis
>>>  
>>> <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#Poweranalysis>
>>>  
>>> 
>>> 1. see above
>>> 2. yes, also time points can miss from the middle. If you have mainly 
>>> missing time points at the end, this will bias your analysis to some 
>>> extend, as the remaining ones may be extremely healthy, as probably the 
>>> more diseased ones drop out. You may want to do a time-to-event (or 
>>> survival-analysis) which considers early drop-out.
>> 
>> Is there any way to do with Freesurfer this kind of analysis ?
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/SurvivalAnalysis 
> <https://surfer.nmr.mgh.harvard.edu/fswiki/SurvivalAnalysis> 
> Yes, there is also a paper where we do this. It is a combination of LME and 
> Survival Analysis (as for the SA you need to have measurements of all 
> subjects at all time points, so you estimate that from the LME model). 

Thank you for the link, I will take a look at. So if understand, this analysis 
has to be done after LME statistical analysis ? Thereafter since SA need all 
time points, LME model will allow me to estimate missing time points ?

> 
>> 
>>> 3. see above (power analysis)
>>> 4. GIGO means garbage in, garbage out, so the less you QC, the more likely 
>>> will your results be junk. The more you QC the less likely will it be junk, 
>>> but could still be. The FS wiki has lots of tutorial information on 
>>> checking freesurfer recons. For longitudinal, you should additionally check 
>>> the surfaces in the base, the brain mask in the base, and the alignment of 
>>> the time points (although there is some wiggle space for the alignment, as 
>>> most things are allowed to evolve further for each time point). 
>> 
>> For the alignment of the time points, should I better comparing brainmask or 
>> norm.mgz ?
> 
> It does not really matter, I would use norm.mgz. I would load images on top 
> of each other and then use the opacity slider in Freeview to blend between 
> them (that way the eye can pick up small motions). I would not worry too much 
> about local deformations which could be caused by non-linearity (gradient). 
> But if you see global misalignment (rotation, translation) it is a cause for 
> concern) .

Ok thank you. The non-linearity you are talking about are well provoked by MRI 
system and not non-linear registration between time points and template base, 
aren’t they ?

Best regards,
Matthieu

> 
>> 
>> In order to avoid bias by adding further time points in the model by the 
>> -add recon all command, is this better for each subject to take into account 
>> all the time points existing for it or only the ones that I will include in 
>> the model (three time points / subject ; if existing 6 time points for any 
>> subject ?)
>> 
> 
> Usually it is recommended to run all time points in the model (so a base with 
> 6 time points) and not use the - - add flag. Also, Linear Mixed Effects 
> models deal well with missing time points. It is perfectly OK to have 
> differently many time points per subject for that. You should still check if 
> there is a bias (e.g. one group always has 3 time points the other 6) that 
> would not be good. Maybe also consult with a local biostatistician if you are 
> not comfortable with the stats. The LME tools are matlab, and so are the 
> survival-analysis scripts. 
> 
> Best, Martin
> 
> 
> 
>> Best regards,
>> Matthieu
>> 
>>> 
>>> Best, Martin
>>> 
>>>> On Nov 21, 2016, at 7:07 PM, Matthieu Vanhoutte 
>>>> mailto:matthieu

Re: [Freesurfer] Longitudinal stream : LME and limits of model

[Matthieu Vanhoutte]

Dear FS's experts,

Could you answer me about questions from below inline precedent mail ?

Best regards,
Matthieu


2016-11-22 21:31 GMT+01:00 Matthieu Vanhoutte :

> Hi Martin,
>
> Please see inline below:
>
> Le 22 nov. 2016 à 17:04, Martin Reuter  a
> écrit :
>
> Hi Matthieu,
> (also inline)
>
> On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> wrote:
>
> Hi Martin,
>
> Thanks for replying. Please see inline below:
>
> Le 21 nov. 2016 à 20:26, Martin Reuter  a
> écrit :
>
> Hi Matthieu,
>
> a few quick answers. Maybe Jorge knows more.
> Generally number of subjects / time points etc. cannot be specified
> generally. All depends on how noisy your data is and how large the effect
> is that you expect to detect. You can do a power analysis in order to
> figure out how many subject / time points would be needed. There are some
> tools for that in the LME toolbox:
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#
> Poweranalysis
>
> 1. see above
> 2. yes, also time points can miss from the middle. If you have mainly
> missing time points at the end, this will bias your analysis to some
> extend, as the remaining ones may be extremely healthy, as probably the
> more diseased ones drop out. You may want to do a time-to-event (or
> survival-analysis) which considers early drop-out.
>
>
> Is there any way to do with Freesurfer this kind of analysis ?
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/SurvivalAnalysis
> Yes, there is also a paper where we do this. It is a combination of LME
> and Survival Analysis (as for the SA you need to have measurements of all
> subjects at all time points, so you estimate that from the LME model).
>
>
>
Thank you for the link, I will take a look at. So if understand, this
analysis has to be done after LME statistical analysis ? Thereafter since
SA need all time points, LME model will allow me to estimate missing time
points ?


>
>
>
> 3. see above (power analysis)
> 4. GIGO means garbage in, garbage out, so the less you QC, the more likely
> will your results be junk. The more you QC the less likely will it be junk,
> but could still be. The FS wiki has lots of tutorial information on
> checking freesurfer recons. For longitudinal, you should additionally check
> the surfaces in the base, the brain mask in the base, and the alignment of
> the time points (although there is some wiggle space for the alignment, as
> most things are allowed to evolve further for each time point).
>
>
> For the alignment of the time points, should I better comparing brainmask
> or norm.mgz ?
>
>
> It does not really matter, I would use norm.mgz. I would load images on
> top of each other and then use the opacity slider in Freeview to blend
> between them (that way the eye can pick up small motions). I would not
> worry too much about local deformations which could be caused by
> non-linearity (gradient). But if you see global misalignment (rotation,
> translation) it is a cause for concern) .
>
>
>
 Ok thank you. The non-linearity you are talking about are well provoked by
MRI system and not non-linear registration between time points and template
base, aren’t they ?


>
>
> In order to avoid bias by adding further time points in the model by the
> -add recon all command, is this better for each subject to take into
> account all the time points existing for it or only the ones that I will
> include in the model (three time points / subject ; if existing 6 time
> points for any subject ?)
>
>
> Usually it is recommended to run all time points in the model (so a base
> with 6 time points) and not use the - - add flag. Also, Linear Mixed
> Effects models deal well with missing time points. It is perfectly OK to
> have differently many time points per subject for that. You should still
> check if there is a bias (e.g. one group always has 3 time points the other
> 6) that would not be good. Maybe also consult with a local biostatistician
> if you are not comfortable with the stats. The LME tools are matlab, and so
> are the survival-analysis scripts.
>
> Best, Martin
>
>
>
> Best regards,
> Matthieu
>
>
> Best, Martin
>
> On Nov 21, 2016, at 7:07 PM, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> wrote:
>
> Dear Freesurfer’s experts,
>
> I would have some questions regarding the LME model to be used in
> longitudinal stream:
>
> 1) Which are the ratio limits or % of missing timepoints accepted ?
> (according time, I have less and less subjects time points)
>
> 2) Is it possible to include patients that would miss the first timepoint
> but got the others ?
>
> 3) C

[Freesurfer] Tracula error ? set: Variable name must begin with a letter

[Matthieu Vanhoutte]

Hello experts,


I am running the first pre-processing
step in Tracula on FS 5.1 and come across the error:

*set: Variable name must begin with a
letter*

I have attached my dmrirc file. Did I make a mistake in this file?

Best regards,

Matthieu


dmrirc.tutorial
Description: Binary data
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Re: [Freesurfer] Tracula error ? set: Variable name must begin with a letter

[Matthieu Vanhoutte]

Hi Anastasia,

I have taken this original file in "*FSDIR5.1/bin/dmrirc.example"* and
modify into "dmrirc.tutorial", so this is meant for use with the version of
tracula that's in 5.1 ?

I will switch to the last version, but before this I'd like to succeed
launching tracula on 5.1...

Best,

Matthieu


2013/12/11 Anastasia Yendiki 

>
> Hi Matthieu - This sample dmrirc file is meant for use with the version of
> tracula that's in 5.3, not 5.1. I would strongly recommend switching to
> that version of tracula anyway, due to improvements in performance and
> speed.
>
> a.y
>
>
> On Wed, 11 Dec 2013, Matthieu Vanhoutte wrote:
>
>  Hello experts,
>>
>> I am running the first pre-processing
>> step in Tracula on FS 5.1 and come across the error:
>>
>> set: Variable name must begin with a
>> letter
>>
>> I have attached my dmrirc file. Did I make a mistake in this file?
>> Best regards,
>>
>> Matthieu
>>
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] Tracula error ? set: Variable name must begin with a letter

[Matthieu Vanhoutte]

Hi Anastasia,

You were right ! I fixed ncpts = 5 for all 18 tracts and th preprocessing
step runs.

Thanks,
Matthieu


2013/12/11 Anastasia Yendiki 

>
> Hi Matthieu - In 5.1 the number of control points (ncpts) was only one
> number, the same for all 18 tracts. Not sure if this is what's causing the
> error.
>
>
> a.y
>
> On Wed, 11 Dec 2013, Matthieu Vanhoutte wrote:
>
>  Hi Anastasia,
>> I have taken this original file in "FSDIR5.1/bin/dmrirc.example" and
>> modify
>> into "dmrirc.tutorial", so this is meant for use with the version of
>> tracula
>> that's in 5.1 ?
>>
>> I will switch to the last version, but before this I'd like to succeed
>> launching tracula on 5.1...
>>
>> Best,
>>
>> Matthieu
>>
>>
>> 2013/12/11 Anastasia Yendiki 
>>
>>   Hi Matthieu - This sample dmrirc file is meant for use with the
>>   version of tracula that's in 5.3, not 5.1. I would strongly
>>   recommend switching to that version of tracula anyway, due to
>>   improvements in performance and speed.
>>
>>   a.y
>>
>>   On Wed, 11 Dec 2013, Matthieu Vanhoutte wrote:
>>
>> Hello experts,
>>
>> I am running the first pre-processing
>> step in Tracula on FS 5.1 and come across the
>> error:
>>
>> set: Variable name must begin with a
>> letter
>>
>> I have attached my dmrirc file. Did I make a mistake
>> in this file?
>> Best regards,
>>
>> Matthieu
>>
>>
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] Tracula error when running bedpostX (2nd step af trac-all)

[Matthieu Vanhoutte]

Dear experts,

To complete my error, I've got moreover another error in
"dmri.bedpostX/logs" for each slice :

*** ERROR (nifti_image_read): failed to find header file for
'/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_'*
*** ERROR:
nifti_image_open(/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_):
bad header info*
*Error: failed to open file
/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_*
*ERROR: Could not open image
/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_*
*Image Exception : #22 :: Failed to read volume
/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_*



*An exception has been thrown*
*Failed to read volume
/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_Trace:
read_volume4DROI.*

Thanks for helping !

Matthieu


2013/12/12 Matthieu Vanhoutte 

> Hello experts,
>
>
> I am running the ball-and-stick model fit in Tracula on FS 5.1 and come 
> across the error:
>
>
> *WARN: Running FSL's bedbost locally - this might take a while
> WARN: It is recommended to run this step on a cluster
> bedpostx_seychelles /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri
> subjectdir is /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri
> Making bedpostx directory structure
> Queuing preprocessing stages
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected 
> operator
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 263: [: SGE: unexpected 
> operator
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx_pre: 
> unexpected operator
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x: unexpected 
> operator
> Queuing parallel processing stage
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected 
> operator
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx: 
> unexpected operator
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x66: unexpected 
> operator
> Queuing post processing stage
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected 
> operator
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 263: [: SGE: unexpected 
> operator
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx_post: 
> unexpected operator
> /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x: unexpected 
> operator
>
> Type /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri.bedpostX/monitor to show 
> progress.
> Type /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri.bedpostX/cancel to 
> terminate all the queued tasks.
>
> You will get an email at the end of the post-processing stage.
> *
>
> I have attached my dmrirc file and trac-all.log.
>
> Best regards,
>
> Matthieu
>
>
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Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

[Matthieu Vanhoutte]

Hello Martin,

Could you please find any time to answer me ?

Many thanks !

Best regards,

Matthieu
Le 30 sept. 2015 13:57, "Matthieu Vanhoutte" 
a écrit :

> Hi Martin,
>
> Thank you for helping !
>
> 1) What should I use for the parameter estimation: "mass univariate" or Novel
> mass-univariate tools (spatiotemporal models)" ?
>
> 2) I have one group of subjects with different timepoints (non equally
> spaced and different numbers of timepoints), and would like to see the
> significant change of FA according to time. Will LME study allow me to get
> this change and how to define contrast to assess it ? Are the results of
> this longitudinal study directionals, i.e. is it possible to establish an
> increase or decrease of FA in significant regions according to time ?
>
> 3) Should the covariates (age, gender...) be demeaned or centered ?
>
> 4) Has the accurate time variable to be in years absolutely or could it
> be also in days ?
>
>
> Best regards,
>
> Matthieu
>
>
> 2015-09-29 17:11 GMT+02:00 Martin Reuter :
>
>> Hi Matthieu,
>>
>> use lme_mass_fit_vw and the y is a simple vector. I would mask the image
>> before doing this and only pass the brain voxels (to increase speed and
>> reduce comparisons).
>>
>> Best, Martin
>>
>>
>> On 09/29/2015 10:43 AM, Matthieu Vanhoutte wrote:
>>
>> Hi Martin,
>>
>> I understand for the multiple comparisons problem. But if I consider a
>> voxel-by-voxel analysis just as hippocampal volume (lme_fit_FS for
>> estimation), how could I consider a correction for multiple comparisons in
>> this univariate case ?
>>
>> Shouldn't I use the lme_mass_fit or lme_mass_fit_vw functions in my mass
>> univariate case ? If yes, how do I have to format my 3D FA volume as input
>> of the LME toolbox ?
>>
>> Best regards,
>>
>> Matthieu
>>
>> -
>> Matthieu Vanhoutte, MSc
>> Research Engineer - Department of Neuroradiology
>> Regional University Hospital, Lille, France
>>
>> 2015-09-29 16:34 GMT+02:00 Martin Reuter :
>>
>>> Hi Matthieu,
>>>
>>> yes, multiple comparisons are a problem for any mass univariate
>>> approach. You can use the FDR2 correction (in the lme matlab tools) which
>>> is less conservative than standard FDR. You can also work in specific ROI's
>>> and average there, to reduce the number of comparisons.
>>>
>>> Best, Martin
>>>
>>>
>>> On 09/29/2015 09:11 AM, Matthieu Vanhoutte wrote:
>>>
>>> Hi Martin,
>>>
>>> Thank you for your answer.
>>>
>>> However, I would like to consider FA maps as a mass-univariate problem
>>> and not a univariate voxel-by-voxel as hippocampal volume. Indeed, my
>>> voxels aren't independant, are they ? So, how to correct for multiple
>>> comparisons then ?
>>>
>>> Best regards,
>>>
>>> Matthieu
>>>
>>> 2015-09-29 15:04 GMT+02:00 Martin Reuter :
>>>
>>>> Hi Matthieu,
>>>>
>>>> if all your images are perfectly registered, you can do LME on a
>>>> voxel-by-voxel basis, just as if you had hippocampal volume or any other
>>>> ROI measure.
>>>>
>>>> Best, Martin
>>>>
>>>>
>>>> On 09/29/2015 06:46 AM, Matthieu Vanhoutte wrote:
>>>>
>>>> Dear experts,
>>>>
>>>> I would like to know if it is possible to make a longitudinal study
>>>> with LME toolbox from volume FA maps registered in a common space ?
>>>>
>>>> I don't have T1 images so the recon-all process couldn't be processed.
>>>> But if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels
>>>> format, could it be in good way for LME ?
>>>>
>>>> Thanks for helping !
>>>>
>>>> Best regards,
>>>>
>>>> Matthieu
>>>>
>>>>
>>>> ___
>>>> Freesurfer mailing 
>>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> --
>>>> Martin Reuter, PhD
>>>> Assistant Professor of Radiology, Harvard Medical School
>>>> Assistant Professor of Neurology, Harvard Medical School
>>>> A.A.Martinos Center for Biomedical Imaging
>>>> Massachusetts General Ho

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

[Matthieu Vanhoutte]

Dear experts,

Could anyone please help me ? My group has small size (7 subjects) with non
equally spaced different timepoints (from 2 up to 4).

Best regards,

Matthieu
Le 30 sept. 2015 13:57, "Matthieu Vanhoutte" 
a écrit :

> Hi Martin,
>
> Thank you for helping !
>
> 1) What should I use for the parameter estimation: "mass univariate" or Novel
> mass-univariate tools (spatiotemporal models)" ?
>
> 2) I have one group of subjects with different timepoints (non equally
> spaced and different numbers of timepoints), and would like to see the
> significant change of FA according to time. Will LME study allow me to get
> this change and how to define contrast to assess it ? Are the results of
> this longitudinal study directionals, i.e. is it possible to establish an
> increase or decrease of FA in significant regions according to time ?
>
> 3) Should the covariates (age, gender...) be demeaned or centered ?
>
> 4) Has the accurate time variable to be in years absolutely or could it
> be also in days ?
>
>
> Best regards,
>
> Matthieu
>
>
> 2015-09-29 17:11 GMT+02:00 Martin Reuter :
>
>> Hi Matthieu,
>>
>> use lme_mass_fit_vw and the y is a simple vector. I would mask the image
>> before doing this and only pass the brain voxels (to increase speed and
>> reduce comparisons).
>>
>> Best, Martin
>>
>>
>> On 09/29/2015 10:43 AM, Matthieu Vanhoutte wrote:
>>
>> Hi Martin,
>>
>> I understand for the multiple comparisons problem. But if I consider a
>> voxel-by-voxel analysis just as hippocampal volume (lme_fit_FS for
>> estimation), how could I consider a correction for multiple comparisons in
>> this univariate case ?
>>
>> Shouldn't I use the lme_mass_fit or lme_mass_fit_vw functions in my mass
>> univariate case ? If yes, how do I have to format my 3D FA volume as input
>> of the LME toolbox ?
>>
>> Best regards,
>>
>> Matthieu
>>
>> -
>> Matthieu Vanhoutte, MSc
>> Research Engineer - Department of Neuroradiology
>> Regional University Hospital, Lille, France
>>
>> 2015-09-29 16:34 GMT+02:00 Martin Reuter :
>>
>>> Hi Matthieu,
>>>
>>> yes, multiple comparisons are a problem for any mass univariate
>>> approach. You can use the FDR2 correction (in the lme matlab tools) which
>>> is less conservative than standard FDR. You can also work in specific ROI's
>>> and average there, to reduce the number of comparisons.
>>>
>>> Best, Martin
>>>
>>>
>>> On 09/29/2015 09:11 AM, Matthieu Vanhoutte wrote:
>>>
>>> Hi Martin,
>>>
>>> Thank you for your answer.
>>>
>>> However, I would like to consider FA maps as a mass-univariate problem
>>> and not a univariate voxel-by-voxel as hippocampal volume. Indeed, my
>>> voxels aren't independant, are they ? So, how to correct for multiple
>>> comparisons then ?
>>>
>>> Best regards,
>>>
>>> Matthieu
>>>
>>> 2015-09-29 15:04 GMT+02:00 Martin Reuter :
>>>
>>>> Hi Matthieu,
>>>>
>>>> if all your images are perfectly registered, you can do LME on a
>>>> voxel-by-voxel basis, just as if you had hippocampal volume or any other
>>>> ROI measure.
>>>>
>>>> Best, Martin
>>>>
>>>>
>>>> On 09/29/2015 06:46 AM, Matthieu Vanhoutte wrote:
>>>>
>>>> Dear experts,
>>>>
>>>> I would like to know if it is possible to make a longitudinal study
>>>> with LME toolbox from volume FA maps registered in a common space ?
>>>>
>>>> I don't have T1 images so the recon-all process couldn't be processed.
>>>> But if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels
>>>> format, could it be in good way for LME ?
>>>>
>>>> Thanks for helping !
>>>>
>>>> Best regards,
>>>>
>>>> Matthieu
>>>>
>>>>
>>>> ___
>>>> Freesurfer mailing 
>>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> --
>>>> Martin Reuter, PhD
>>>> Assistant Professor of Radiology, Harvard Medical School
>>>> Assistant Professor of Neurology, Harvard Medical School
>>>> A.A.Martinos Center f

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

[Matthieu Vanhoutte]

Hello Martin,

Many thanks for your answer !

Indeed, I didn't add age and gender as covariates according the fact of my
small number of patients group. Moreover, I couldn't put the slope as a
random effect because of no convergence problem...

Concerning the convergence, at the end of the estimation model with only
one random effect on intercept, I got this error :



*Summary:Algorithm did not converge at 9.1964 percent of the total number
of locations.Total elapsed time is 46.692 minutes.*

1) Is this challenging me about the validity of the results ?
2) Do you know a mean to avoid or take account of spurious effects (due to
violation of the assumption of gaussian noise) in the statistical analysis
results ?

Best regards,

Matthieu

2015-10-13 15:26 GMT+02:00 Martin Reuter :

> Hi Matthieu,
>
> 1. The spatiotemporal approach is designed for surfaces, not for voxel
> images, so regular mass univariate (vw).
> 2. Yes, that can be done with LME. 1 group is a simple design: column of
> 1, colum of time_from_baseline, other covariates such as age (I would not
> include too many as you only have very few subjects). Then set the
> intercept as random effect and test for a slope effect (2nd column). You
> can also play around with setting slope as random effect, but with only 7
> subjects, not sure. You can do a model comparison as described on our wiki.
> 3. Not sure if I would include gender (unless there is good reason for
> that). You are looking at within subject slopes. I don't think you need to
> demean age.
> 4. does not matter. If you look at the betas they will be in unit/days or
> unit/years (or week , month) depending on your decision.
>
> The danger with such a small group is that outliers will affect your
> results a lot (they severely violate the assumption of gaussian noise) and
> can produce spurious effects.
>
> Best, Martin
>
>
>
> On 10/11/2015 04:31 PM, Matthieu Vanhoutte wrote:
>
> Dear experts,
>
> Could anyone please help me ? My group has small size (7 subjects) with
> non equally spaced different timepoints (from 2 up to 4).
>
> Best regards,
>
> Matthieu
> Le 30 sept. 2015 13:57, "Matthieu Vanhoutte" 
> a écrit :
>
>> Hi Martin,
>>
>> Thank you for helping !
>>
>> 1) What should I use for the parameter estimation: "mass univariate" or Novel
>> mass-univariate tools (spatiotemporal models)" ?
>>
>> 2) I have one group of subjects with different timepoints (non equally
>> spaced and different numbers of timepoints), and would like to see the
>> significant change of FA according to time. Will LME study allow me to get
>> this change and how to define contrast to assess it ? Are the results of
>> this longitudinal study directionals, i.e. is it possible to establish an
>> increase or decrease of FA in significant regions according to time ?
>>
>> 3) Should the covariates (age, gender...) be demeaned or centered ?
>>
>> 4) Has the accurate time variable to be in years absolutely or could it
>> be also in days ?
>>
>>
>> Best regards,
>>
>> Matthieu
>>
>>
>> 2015-09-29 17:11 GMT+02:00 Martin Reuter < 
>> mreu...@nmr.mgh.harvard.edu>:
>>
>>> Hi Matthieu,
>>>
>>> use lme_mass_fit_vw and the y is a simple vector. I would mask the image
>>> before doing this and only pass the brain voxels (to increase speed and
>>> reduce comparisons).
>>>
>>> Best, Martin
>>>
>>>
>>> On 09/29/2015 10:43 AM, Matthieu Vanhoutte wrote:
>>>
>>> Hi Martin,
>>>
>>> I understand for the multiple comparisons problem. But if I consider a
>>> voxel-by-voxel analysis just as hippocampal volume (lme_fit_FS for
>>> estimation), how could I consider a correction for multiple comparisons in
>>> this univariate case ?
>>>
>>> Shouldn't I use the lme_mass_fit or lme_mass_fit_vw functions in my mass
>>> univariate case ? If yes, how do I have to format my 3D FA volume as input
>>> of the LME toolbox ?
>>>
>>> Best regards,
>>>
>>> Matthieu
>>>
>>> -
>>> Matthieu Vanhoutte, MSc
>>> Research Engineer - Department of Neuroradiology
>>> Regional University Hospital, Lille, France
>>>
>>> 2015-09-29 16:34 GMT+02:00 Martin Reuter < 
>>> mreu...@nmr.mgh.harvard.edu>:
>>>
>>>> Hi Matthieu,
>>>>
>>>> yes, multiple comparisons are a problem for any mass univariate
>>>> approach. You can use the FDR2 c

[Freesurfer] Recon-all -bigventricles option : general use or not in Alzheimer cases ?

[Matthieu Vanhoutte]

Dear FreeSurfer experts,

My question is in the title. I'm working on Alzheimer case where most of
the cases have large ventricles. Is it better in general use to apply
-bigventricles option on all subjects (for homogeneous calculus or
something like that...) or to distinct subtle cases of patients with not so
big ventricles ?

Thanks in advance for helping !

Best regards,

Matthie
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Re: [Freesurfer] Recon-all -bigventricles option : general use or not in Alzheimer cases ?

[Matthieu Vanhoutte]

Hi Bruce,

Exactly I want to be sure that I process my data in the same way, so not
introduce bias with partially use of -bigventricles option.

1) I tried the recon-all process on AD patient with big ventricles and
atrophy with and without the -bigventricles option. I am not pretty sure of
which process is the best in terms of segmentation according the aseg.mgz ?
(I'll send you T1 and aseg.mgz for the two process)
2) Considering cortical atrophy, a lot of gray matter hasn't been taken
account in the cortex segmentation. Is there an automatic way to improve
the cortical segmentation in case of visible atrophy ?

Best regards,
Matthieu

2015-12-03 18:03 GMT+01:00 Bruce Fischl :

> Hi Matthie
>
> do you find that it doesn't work well without bigventricles? You just
> want to be sure that you process your data in the same way so there is no
> bias in the results. We have found that most early AD cases work fine
> without needing special flags. It's more for late stage AD or hydrocephalus
> and such.
>
> cheers
> Bruce
>
>
>
> On Thu, 3 Dec 2015, Matthieu
> Vanhoutte wrote:
>
> > Dear FreeSurfer experts,
> >
> > My question is in the title. I'm working on Alzheimer case where most of
> the cases have large
> > ventricles. Is it better in general use to apply -bigventricles option
> on all subjects (for
> > homogeneous calculus or something like that...) or to distinct subtle
> cases of patients with not so
> > big ventricles ?
> >
> > Thanks in advance for helping !
> >
> > Best regards,
> >
> > Matthie
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***

[Matthieu Vanhoutte]

Dear experts,

I am confronted with some problem in the "recon-all" of a few subjects
concerning Talairach space, but don't know how to manage these.

Please find below the recon-all log with errors :

#
#@# Talairach Failure Detection Fri Dec  4 15:29:38 CET 2015
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6911,
pval=0.4932 >= threshold=0.0050)

 awk -f /home/global//freesurfer5.3//bin/extract_talairach_avi_QA.awk
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log


 tal_QC_AZS
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log

TalAviQA: 0.93027
z-score: -10
ERROR: Talairach QA check failed!
   z-score = -10 <= -9 = threshold
   atlas xform error = 0 < -60 | > 24
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Attempting MINC mritotal to perform Talairach align
#
#@# Talairach Fri Dec  4 15:29:39 CET 2015
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz


 talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm

/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
/home/global//freesurfer5.3//bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $
Linux wutang 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux
Fri Dec  4 15:31:35 CET 2015
tmpdir is transforms/tmp.talairach.13347
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.13347/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.13347/src.mnc
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig_nu.mgz...
TR=9.90, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (7.45058e-09, 1, 0)
writing to transforms/tmp.talairach.13347/src.mnc...

mritotal -verbose -debug -clobber -modeldir
/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg -protocol icbm
transforms/tmp.talairach.13347/src.mnc transforms/talairach.auto.xfm


Fri Dec  4 15:31:58 CET 2015
talairach done

 cp transforms/talairach.auto.xfm transforms/talairach.xfm

#
#@# Talairach Failure Detection Fri Dec  4 15:31:59 CET 2015
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0039, pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Linux wutang 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s M0_2011-02-23 exited with ERRORS at Fri Dec  4 15:32:00 CET
2015

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Thanks in advance for helping !

Best regards,
Matthieu
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Re: [Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***

[Matthieu Vanhoutte]

Dear FS experts,

I got no answer to my question. Could anyone explain me what is the problem
and how to solve it ?

Best regards,
Matthieu

2015-12-04 16:11 GMT+01:00 Matthieu Vanhoutte :

> Dear experts,
>
> I am confronted with some problem in the "recon-all" of a few subjects
> concerning Talairach space, but don't know how to manage these.
>
> Please find below the recon-all log with errors :
>
> #
> #@# Talairach Failure Detection Fri Dec  4 15:29:38 CET 2015
> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
>
>  talairach_afd -T 0.005 -xfm transforms/talairach.xfm
>
> talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6911,
> pval=0.4932 >= threshold=0.0050)
>
>  awk -f /home/global//freesurfer5.3//bin/extract_talairach_avi_QA.awk
> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log
>
>
>  tal_QC_AZS
> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log
>
> TalAviQA: 0.93027
> z-score: -10
> ERROR: Talairach QA check failed!
>z-score = -10 <= -9 = threshold
>atlas xform error = 0 < -60 | > 24
> Manual Talairach alignment may be necessary, or
> include the -notal-check flag to skip this test,
> making sure the -notal-check flag follows -all
> or -autorecon1 in the command string.
> See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> INFO: Attempting MINC mritotal to perform Talairach align
> #
> #@# Talairach Fri Dec  4 15:29:39 CET 2015
> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
>
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
> --i orig.mgz --o orig_nu.mgz
>
>
>  talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>
> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
> /home/global//freesurfer5.3//bin/talairach
> --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
> $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $
> Linux wutang 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014
> x86_64 x86_64 x86_64 GNU/Linux
> Fri Dec  4 15:31:35 CET 2015
> tmpdir is transforms/tmp.talairach.13347
> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
> mri_convert orig_nu.mgz transforms/tmp.talairach.13347/src.mnc
> mri_convert orig_nu.mgz transforms/tmp.talairach.13347/src.mnc
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from orig_nu.mgz...
> TR=9.90, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (7.45058e-09, 1, 0)
> writing to transforms/tmp.talairach.13347/src.mnc...
> 
> mritotal -verbose -debug -clobber -modeldir
> /home/global//freesurfer5.3//mni/bin/../share/mni_autoreg -protocol icbm
> transforms/tmp.talairach.13347/src.mnc transforms/talairach.auto.xfm
>
>
> Fri Dec  4 15:31:58 CET 2015
> talairach done
>
>  cp transforms/talairach.auto.xfm transforms/talairach.xfm
>
> #
> #@# Talairach Failure Detection Fri Dec  4 15:31:59 CET 2015
> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
>
>  talairach_afd -T 0.005 -xfm transforms/talairach.xfm
>
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0.0039, pval=0. < threshold=0.0050)
> Manual Talairach alignment may be necessary, or
> include the -notal-check flag to skip this test,
> making sure the -notal-check flag follows -all
> or -autorecon1 in the command string.
> See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> Linux wutang 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s M0_2011-02-23 exited with ERRORS at Fri Dec  4 15:32:00 CET
> 2015
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> Thanks in advance for helping !
>
> Best regards,
> Matthieu
>
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Re: [Freesurfer] Recon-all -bigventricles option : general use or not in Alzheimer cases ?

[Matthieu Vanhoutte]

Hi Bruce,

I got no answer to my questions below with files provided thanks to
FileDrop.

Could you tell me if you received these questions and associated files ?

Thanks in advance !

Best regards,
Matthieu

2015-12-04 15:17 GMT+01:00 Matthieu Vanhoutte :

> Hi Bruce,
>
> Exactly I want to be sure that I process my data in the same way, so not
> introduce bias with partially use of -bigventricles option.
>
> 1) I tried the recon-all process on AD patient with big ventricles and
> atrophy with and without the -bigventricles option. I am not pretty sure of
> which process is the best in terms of segmentation according the aseg.mgz ?
> (I'll send you T1 and aseg.mgz for the two process)
> 2) Considering cortical atrophy, a lot of gray matter hasn't been taken
> account in the cortex segmentation. Is there an automatic way to improve
> the cortical segmentation in case of visible atrophy ?
>
> Best regards,
> Matthieu
>
>
> 2015-12-03 18:03 GMT+01:00 Bruce Fischl :
>
>> Hi Matthie
>>
>> do you find that it doesn't work well without bigventricles? You just
>> want to be sure that you process your data in the same way so there is no
>> bias in the results. We have found that most early AD cases work fine
>> without needing special flags. It's more for late stage AD or
>> hydrocephalus
>> and such.
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Thu, 3 Dec 2015, Matthieu
>> Vanhoutte wrote:
>>
>> > Dear FreeSurfer experts,
>> >
>> > My question is in the title. I'm working on Alzheimer case where most
>> of the cases have large
>> > ventricles. Is it better in general use to apply -bigventricles option
>> on all subjects (for
>> > homogeneous calculus or something like that...) or to distinct subtle
>> cases of patients with not so
>> > big ventricles ?
>> >
>> > Thanks in advance for helping !
>> >
>> > Best regards,
>> >
>> > Matthie
>> >
>> >
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Re: [Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***

[Matthieu Vanhoutte]

Hi Bruce,

I tried to follow the tutorial :
http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview

But nothing appeared in the image window of tkregister2 command... Below
you'll find the log of the command :

tkregister2 --mgz --s M0_2010-03-25 --fstal
tkregister_tcl /home/global//freesurfer5.3//tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume (null)
reg file   (null)
LoadVol1
ZeroCRAS   1
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1

%Fri Dec  4 15:13:39 2015>>> /home/global//freesurfer5.3//mni/bin/minctracc
-clobber -debug /tmp/1504527.1.M32_q/mritotal_31071/src_8_dxyz.mnc
/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
transforms/talairach.auto.xfm -transformation
/tmp/1504527.1.M32_q/mritotal_31071/src_8tmp2c.xfm -lsq9 -xcorr -model_mask
/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_mask.mnc
-center 5.23 17.591406 -32.821045 -step 4 4 4 -tol 0.004 -simplex 2

talairach.xfm -
 0.708   0.183  -0.254  -31.077;
-0.311   0.477  -0.525  -62.791;
 0.033   0.582   0.509   156.288;
 0.000   0.000   0.000   1.000;
INFO: loading target /NAS/tupac/matthieu/FS5.3/M0_2010-03-25/mri/orig.mgz
Zeroing CRAS of target
new xfm -
 0.708   0.183  -0.254  -25.242;
-0.311   0.477  -0.525  -57.556;
 0.033   0.582   0.509   165.535;
 0.000   0.000   0.000   1.000;
-
INFO: changing target type to float
Ttarg: 
-1.000  -0.000   0.000   128.000;
-0.000  -0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/global//freesurfer5.3//average/mni305.cor.mgz
INFO: changing move type to float
Tmov: 
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
 Input registration matrix 
 0.708   0.183  -0.254  -25.242;
-0.311   0.477  -0.525  -57.556;
 0.033   0.582   0.509   165.535;
 0.000   0.000   0.000   1.000;
Determinant 0.464133
subject = M0_2010-03-25
Zoom Factor = 2, SQR() = 4
FOV = 256
Opening window M0_2010-03-25
Opening M0_2010-03-25, xnum = 256, xdim = 512
Setting scale
tkregister2: interface: /home/global//freesurfer5.3//tktools/tkregister2.tcl
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}

T1.mgz, brainmask.mgz and subject's surfaces haven't been created yet. I
have checked that my input volume has the correct direction cosines.

Could you explain me what's wrong ?

Thanks !

Best regards,
Matthieu

2015-12-08 22:08 GMT+01:00 Bruce Fischl :

> Hi Matthieu
>
> did you check the talairach registration as suggested? ALso, make sure
> that your input volume has the correct direction cosines (that is, that
> what freeview thinks is anterior is actually anterior, etc...)
> cheers
> Bruce
>
>
>
> On Tue, 8 Dec 2015, Matthieu Vanhoutte wrote:
>
> Dear FS experts,
>>
>> I got no answer to my question. Could anyone explain me what is the
>> problem and how to solve it ?
>>
>> Best regards,
>> Matthieu
>>
>> 2015-12-04 16:11 GMT+01:00 Matthieu Vanhoutte <
>> matthieuvanhou...@gmail.com>:
>>   Dear experts,
>>
>> I am confronted with some problem in the "recon-all" of a few subjects
>> concerning Talairach
>> space, but don't know how to manage these.
>>
>> Please find below the recon-all log with errors :
>>
>> #
>> #@# Talairach Failure Detection Fri Dec  4 15:29:38 CET 2015
>> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
>>
>>  talairach_afd -T 0.005 -xfm transforms/talairach.xfm
>>
>> talairach_afd: Talairach Transform: transforms/talairach.xfm OK
>> (p=0.6911, pval=0.4932 >=
>> threshold=0.0050)
>>
>>  awk -f /home/global//freesurfer5.3//bin/extract_talairach_avi_QA.awk
>> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log
>>
>>
>>  tal_QC_AZS
>> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log
>>
>> TalAviQA: 0.93027
>> z-score: -10
>> ERROR: Talairach QA check failed!
>>z-score = -10 <= -9 = threshold
>>atlas xform error = 0 < -60 | > 24
>> Manual Talairach alignment may be necessary, or
>> include the -notal-check flag to skip this test,
>> making sure the -notal-check flag follows -all
>> or -autorecon1 in the command string.
>> See http://surfer.nmr.mgh.harvard.edu/fs

Re: [Freesurfer] Recon-all get stucked without error during processing

[Matthieu Vanhoutte]

Hi Bruce,

Indeed norm.mgz isn't empty but doesn't look well (truncated and warped).

Is this bug fixed in the v6 beta release ?

If this is the case :
1) Would you advise me to try on the v6 ?
2) Should I so relaunch all recon-all process on my subjects computed with
v5.3  and work only with the v6 beta ?

Best regards,
Matthieu

2015-12-09 15:55 GMT+01:00 Bruce Fischl :

> Hi Matthieu
>
> this might be a bug that is fixed in 6.0. Can you cehck the input to
> mri_cc (norm.mgz) and make sure it is not empty? In older versions if the
> skull stripping failed and generated an empty
> norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang.
>
> cheers
> Bruce
>
> On Wed, 9 Dec 2015,
> Matthieu Vanhoutte wrote:
>
> > Dear FS epxerts,
> >
> > I have launched a recon-all process on a subject. Unfortunately, I tried
> two times but the process get stucked at the same step
> > without error.
> >
> > Please found the recon-all.log associated attached to this mail.
> >
> > Thanks in advance for helping !
> >
> > Best regards,
> > Matthieu
> >
> >
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Re: [Freesurfer] Recon-all get stucked without error during processing

[Matthieu Vanhoutte]

Hi Bruce,

In fact T1.mgz is ok, but the skull stripping failed and seemed to have
taken only the jawbone and the neck.

Best regards,
Matthieu

2015-12-09 16:16 GMT+01:00 Bruce Fischl :

> Hi Matthieu
>
> you need to track backwards and see where the problem started. Why is the
> norm warped? Actaully, it shouldn't be warped, although it might be
> truncated if the skull stripping failed.
>
>
> cheers
> Bruce
> On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote:
>
> Hi Bruce,
>>
>> Indeed norm.mgz isn't empty but doesn't look well (truncated and warped).
>>
>> Is this bug fixed in the v6 beta release ?
>>
>> If this is the case :
>> 1) Would you advise me to try on the v6 ?
>> 2) Should I so relaunch all recon-all process on my subjects computed
>> with v5.3  and work only with the v6 beta ?
>>
>> Best regards,
>> Matthieu
>>
>> 2015-12-09 15:55 GMT+01:00 Bruce Fischl :
>>   Hi Matthieu
>>
>>   this might be a bug that is fixed in 6.0. Can you cehck the input to
>>   mri_cc (norm.mgz) and make sure it is not empty? In older versions
>> if the
>>   skull stripping failed and generated an empty
>>   norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang.
>>
>>   cheers
>>   Bruce
>>
>>   On Wed, 9 Dec 2015,
>>   Matthieu Vanhoutte wrote:
>>
>>   > Dear FS epxerts,
>>   >
>>   > I have launched a recon-all process on a subject. Unfortunately,
>> I tried two times but the process get stucked at
>>   the same step
>>   > without error.
>>   >
>>   > Please found the recon-all.log associated attached to this mail.
>>   >
>>   > Thanks in advance for helping !
>>   >
>>   > Best regards,
>>   > Matthieu
>>   >
>>   >
>> ___
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>>
>>
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[Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Matthieu Vanhoutte]

Dear FS experts,

1) First Is it possible to use the partial volume correction provided in
the v6 beta version of FreeSurfer despite the fact that recon-all have been
done for all subjects with the v5.3 ?

2) Does this method supply an intensity normalisation for PET images ?

Best regards,
Matthieu
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Re: [Freesurfer] Recon-all get stucked without error during processing

[Matthieu Vanhoutte]

Hi Bruce,

Do you have an idea of how to solve this problem of skull stripping (below)
?

Best regards,
Matthieu

2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte :

> Hi Bruce,
>
> In fact T1.mgz is ok, but the skull stripping failed and seemed to have
> taken only the jawbone and the neck.
>
> Best regards,
> Matthieu
>
>
> 2015-12-09 16:16 GMT+01:00 Bruce Fischl :
>
>> Hi Matthieu
>>
>> you need to track backwards and see where the problem started. Why is the
>> norm warped? Actaully, it shouldn't be warped, although it might be
>> truncated if the skull stripping failed.
>>
>>
>> cheers
>> Bruce
>> On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote:
>>
>> Hi Bruce,
>>>
>>> Indeed norm.mgz isn't empty but doesn't look well (truncated and warped).
>>>
>>> Is this bug fixed in the v6 beta release ?
>>>
>>> If this is the case :
>>> 1) Would you advise me to try on the v6 ?
>>> 2) Should I so relaunch all recon-all process on my subjects computed
>>> with v5.3  and work only with the v6 beta ?
>>>
>>> Best regards,
>>> Matthieu
>>>
>>> 2015-12-09 15:55 GMT+01:00 Bruce Fischl :
>>>   Hi Matthieu
>>>
>>>   this might be a bug that is fixed in 6.0. Can you cehck the input
>>> to
>>>   mri_cc (norm.mgz) and make sure it is not empty? In older versions
>>> if the
>>>   skull stripping failed and generated an empty
>>>   norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang.
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Wed, 9 Dec 2015,
>>>   Matthieu Vanhoutte wrote:
>>>
>>>   > Dear FS epxerts,
>>>   >
>>>   > I have launched a recon-all process on a subject. Unfortunately,
>>> I tried two times but the process get stucked at
>>>   the same step
>>>   > without error.
>>>   >
>>>   > Please found the recon-all.log associated attached to this mail.
>>>   >
>>>   > Thanks in advance for helping !
>>>   >
>>>   > Best regards,
>>>   > Matthieu
>>>   >
>>>   >
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>>> properly
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>>>
>>>
>>>
>>>
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Re: [Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***

[Matthieu Vanhoutte]

Hi Bruce,

Do you have an idea of what to do concerning this problem (below) ? I have
re-run with -notal-check and it worked not for all cases

Best regards,
Matthieu

2015-12-09 15:15 GMT+01:00 Matthieu Vanhoutte :

> Hi Bruce,
>
> I tried to follow the tutorial :
> http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview
>
> But nothing appeared in the image window of tkregister2 command... Below
> you'll find the log of the command :
>
> tkregister2 --mgz --s M0_2010-03-25 --fstal
> tkregister_tcl /home/global//freesurfer5.3//tktools/tkregister2.tcl
> INFO: no target volume specified, assuming FreeSurfer orig volume.
> target  volume orig
> movable volume (null)
> reg file   (null)
> LoadVol1
> ZeroCRAS   1
> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> Diagnostic Level -1
>
> %Fri Dec  4 15:13:39 2015>>>
> /home/global//freesurfer5.3//mni/bin/minctracc -clobber -debug
> /tmp/1504527.1.M32_q/mritotal_31071/src_8_dxyz.mnc
> /home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
> transforms/talairach.auto.xfm -transformation
> /tmp/1504527.1.M32_q/mritotal_31071/src_8tmp2c.xfm -lsq9 -xcorr -model_mask
> /home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_mask.mnc
> -center 5.23 17.591406 -32.821045 -step 4 4 4 -tol 0.004 -simplex 2
>
> talairach.xfm -
>  0.708   0.183  -0.254  -31.077;
> -0.311   0.477  -0.525  -62.791;
>  0.033   0.582   0.509   156.288;
>  0.000   0.000   0.000   1.000;
> INFO: loading target /NAS/tupac/matthieu/FS5.3/M0_2010-03-25/mri/orig.mgz
> Zeroing CRAS of target
> new xfm -
>  0.708   0.183  -0.254  -25.242;
> -0.311   0.477  -0.525  -57.556;
>  0.033   0.582   0.509   165.535;
>  0.000   0.000   0.000   1.000;
> -
> INFO: changing target type to float
> Ttarg: 
> -1.000  -0.000   0.000   128.000;
> -0.000  -0.000   1.000  -128.000;
>  0.000  -1.000   0.000   128.000;
>  0.000   0.000   0.000   1.000;
> INFO: loading movable /home/global//freesurfer5.3//average/mni305.cor.mgz
> INFO: changing move type to float
> Tmov: 
> -1.000   0.000   0.000   128.000;
>  0.000   0.000   1.000  -128.000;
>  0.000  -1.000   0.000   128.000;
>  0.000   0.000   0.000   1.000;
> mkheaderreg = 0, float2int = 0
>  Input registration matrix 
>  0.708   0.183  -0.254  -25.242;
> -0.311   0.477  -0.525  -57.556;
>  0.033   0.582   0.509   165.535;
>  0.000   0.000   0.000   1.000;
> Determinant 0.464133
> subject = M0_2010-03-25
> Zoom Factor = 2, SQR() = 4
> FOV = 256
> Opening window M0_2010-03-25
> Opening M0_2010-03-25, xnum = 256, xdim = 512
> Setting scale
> tkregister2: interface:
> /home/global//freesurfer5.3//tktools/tkregister2.tcl
> tkregister.tcl: startup done
> tkregister.tcl: default macro interface (to change: macro,mini,micro)
> tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
>
> T1.mgz, brainmask.mgz and subject's surfaces haven't been created yet. I
> have checked that my input volume has the correct direction cosines.
>
> Could you explain me what's wrong ?
>
> Thanks !
>
> Best regards,
> Matthieu
>
> 2015-12-08 22:08 GMT+01:00 Bruce Fischl :
>
>> Hi Matthieu
>>
>> did you check the talairach registration as suggested? ALso, make sure
>> that your input volume has the correct direction cosines (that is, that
>> what freeview thinks is anterior is actually anterior, etc...)
>> cheers
>> Bruce
>>
>>
>>
>> On Tue, 8 Dec 2015, Matthieu Vanhoutte wrote:
>>
>> Dear FS experts,
>>>
>>> I got no answer to my question. Could anyone explain me what is the
>>> problem and how to solve it ?
>>>
>>> Best regards,
>>> Matthieu
>>>
>>> 2015-12-04 16:11 GMT+01:00 Matthieu Vanhoutte <
>>> matthieuvanhou...@gmail.com>:
>>>   Dear experts,
>>>
>>> I am confronted with some problem in the "recon-all" of a few subjects
>>> concerning Talairach
>>> space, but don't know how to manage these.
>>>
>>> Please find below the recon-all log with errors :
>>>
>>> #
>>> #@# Talairach Failure Detection Fri Dec  4 15:29:38 CET 2015
>>> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
>>>
>>>  talairach_afd -T 0.005 -xfm transforms/talairach.xfm
>>>
>>> talairach_afd: Talairach Transform: transforms/talairach.xfm OK
>>> (p=0.6911, pval=0.4932 >=
>>> t

Re: [Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***

[Matthieu Vanhoutte]

Hi Bruce,

How can I check if I have the correct orientation ? The initial image look
as classical T1 weighted.

I have the problem only on one subject above all, so that sounds like an
exception ?

Best regards,

Matthieu

2015-12-11 14:49 GMT+01:00 Bruce Fischl :

> did it have the correct orientation? Can you explain what the initial
> images were? Usually if you start from dicoms right from the scanner with a
> reasonable scan this isn't a problem so if it's happening frequently then
> it may be that something else is wrong.
>
> cheers
> Bruce
>
>
> On Fri, 11 Dec 2015, Matthieu Vanhoutte wrote:
>
> Hi Bruce,
>>
>> Do you have an idea of what to do concerning this problem (below) ? I have
>> re-run with -notal-check and it worked not for all cases
>>
>> Best regards,
>> Matthieu
>>
>> 2015-12-09 15:15 GMT+01:00 Matthieu Vanhoutte <
>> matthieuvanhou...@gmail.com>:
>>   Hi Bruce,
>>
>> I tried to follow the tutorial :
>> http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview
>>
>> But nothing appeared in the image window of tkregister2 command...
>> Below you'll find the log of the command :
>>
>> tkregister2 --mgz --s M0_2010-03-25 --fstal
>> tkregister_tcl /home/global//freesurfer5.3//tktools/tkregister2.tcl
>> INFO: no target volume specified, assuming FreeSurfer orig volume.
>> target  volume orig
>> movable volume (null)
>> reg file   (null)
>> LoadVol1
>> ZeroCRAS   1
>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
>> Diagnostic Level -1
>>
>> %Fri Dec  4 15:13:39 2015>>>
>> /home/global//freesurfer5.3//mni/bin/minctracc -clobber -debug
>>
>> /tmp/1504527.1.M32_q/mritotal_31071/src_8_dxyz.mnc/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_dxy
>> z.mnc transforms/talairach.auto.xfm -transformation
>> /tmp/1504527.1.M32_q/mritotal_31071/src_8tmp2c.xfm -lsq9 -xcorr
>>
>> -model_mask/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_mas
>> k.mnc -center 5.23 17.591406 -32.821045 -step 4 4 4 -tol 0.004
>> -simplex 2
>>
>> talairach.xfm -
>>  0.708   0.183  -0.254  -31.077;
>> -0.311   0.477  -0.525  -62.791;
>>  0.033   0.582   0.509   156.288;
>>  0.000   0.000   0.000   1.000;
>> INFO: loading target
>> /NAS/tupac/matthieu/FS5.3/M0_2010-03-25/mri/orig.mgz
>> Zeroing CRAS of target
>> new xfm -
>>  0.708   0.183  -0.254  -25.242;
>> -0.311   0.477  -0.525  -57.556;
>>  0.033   0.582   0.509   165.535;
>>  0.000   0.000   0.000   1.000;
>> -
>> INFO: changing target type to float
>> Ttarg: 
>> -1.000  -0.000   0.000   128.000;
>> -0.000  -0.000   1.000  -128.000;
>>  0.000  -1.000   0.000   128.000;
>>  0.000   0.000   0.000   1.000;
>> INFO: loading movable
>> /home/global//freesurfer5.3//average/mni305.cor.mgz
>> INFO: changing move type to float
>> Tmov: 
>> -1.000   0.000   0.000   128.000;
>>  0.000   0.000   1.000  -128.000;
>>  0.000  -1.000   0.000   128.000;
>>  0.000   0.000   0.000   1.000;
>> mkheaderreg = 0, float2int = 0
>>  Input registration matrix 
>>  0.708   0.183  -0.254  -25.242;
>> -0.311   0.477  -0.525  -57.556;
>>  0.033   0.582   0.509   165.535;
>>  0.000   0.000   0.000   1.000;
>> Determinant 0.464133
>> subject = M0_2010-03-25
>> Zoom Factor = 2, SQR() = 4
>> FOV = 256
>> Opening window M0_2010-03-25
>> Opening M0_2010-03-25, xnum = 256, xdim = 512
>> Setting scale
>> tkregister2: interface:
>> /home/global//freesurfer5.3//tktools/tkregister2.tcl
>> tkregister.tcl: startup done
>> tkregister.tcl: default macro interface (to change: macro,mini,micro)
>> tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
>>
>> T1.mgz, brainmask.mgz and subject's surfaces haven't been created yet.
>> I have checked that my input volume has the correct direction cosines.
>>
>> Could you explain me what's wrong ?
>>
>> Thanks !
>>
>> Best regards,
>> Matthieu
>>
>> 2015-12-08 22:08 GMT+01:00 Bruce Fischl :
>>   Hi Matthieu
>>
>>   did you check the talairach registration as suggested?
>>   ALso, make sure that your input volume has the correct
>>   direction cosines (that is, that what freeview thinks is
>>   anterior is actually anterior, etc...)
>>   cheers
&g

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Matthieu Vanhoutte]

Dear experts,

Could anyone answer to my questions below ?

Thanks !

Best regards,
Matthieu

2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte :

> Dear FS experts,
>
> 1) First Is it possible to use the partial volume correction provided in
> the v6 beta version of FreeSurfer despite the fact that recon-all have been
> done for all subjects with the v5.3 ?
>
> 2) Does this method supply an intensity normalisation for PET images ?
>
> Best regards,
> Matthieu
>
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[Freesurfer] Segmentation comparison between FS5.3 and FS6beta

[Matthieu Vanhoutte]

Dear FS's experts,

I have tried the recon-all process on one subject with both FS v5.3 and
v6_beta.

Although subcortical structures seems to be better segmented in v6_beta, I
find that v6_beta over-segmented some other structures as cerebellum,
hippocampus, ...

I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files
for both freesurfer versions.

Could you please look at it and tell me what do you think about and advise
me ?

Thank you !

Best regards,
Matthieu
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Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Matthieu Vanhoutte]

Dear Douglas,

Please see below :

2015-12-15 18:37 GMT+01:00 Douglas N Greve :

>
>
> On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> > Dear experts,
> >
> > Could anyone answer to my questions below ?
> >
> > Thanks !
> >
> > Best regards,
> > Matthieu
> >
> > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
> > mailto:matthieuvanhou...@gmail.com>>:
> >
> > Dear FS experts,
> >
> > 1) First Is it possible to use the partial volume correction
> > provided in the v6 beta version of FreeSurfer despite the fact
> > that recon-all have been done for all subjects with the v5.3 ?
> >
> Yes
>

Great ! but isn't it a problem for computing rSUV with pons as reference
structure since brainstem isn't sub-segmented in the version 5.3 of
recon-all ?


> >
> >
> > 2) Does this method supply an intensity normalisation for PET images
> ?
> >
> What do you mean by intensity normalization? For uptake analysis, people
> usually use SUV (standard uptake values where the whole image is scaled
> by a value related to the injection mass and subject weight) or you
> choose a reference structure to scale by (often called rSUV for
> relative). By default mri_gtmpvc uses pons, but you can choose any
> structure you want with the --rescale flag
>
>
> >
> > Best regards,
> > Matthieu
> >
> >
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
>

Best regards,
Matthieu


> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
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> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

[Matthieu Vanhoutte]

Hi Bruce,

All right then it's only a question of time ofr the new v6 release !

Meanwhile, is it possible and coherent :
1) to use the partial volume correction provided in the v6 beta version of
FreeSurfer despite the fact that recon-all have been done for all subjects
with the v5.3 ?
2) to use sub-segmentations of brainstem and hippocampus provided by v6
beta version of FreeSurfer despite the fact that recon-all have been done
for all subjects with the v5.3 ?

Thanks !

Best regards,
Matthieu

2015-12-15 18:22 GMT+01:00 Bruce Fischl :

> Hi Matthiew
>
> we are still hoping to get an official v6 release out in the next month or
> two, so it would be best to use that which I think will outperform whatever
> beta you have and 5.3. If you can't wait you are probably better off using
> 5.3 (although I think the v6 you have is more  accurate) so that people can
> at least replicate the software version you are using
>
>
> cheers
> Bruce
>
> On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:
>
> Hi Bruce,
>>
>> Is it better to overestimate than underestimate ? Please find joined this
>> two saggital images (FS v5.3 and FS v6_beta) of brain
>> segmentation. Cerebellum in v6_beta really seems to go outside of its
>> borderlines even if cerebellum in v5.3 is indeed lightly
>> underestimated.
>>
>> Looking at the cerebral cortex I found the segmentation less "smoothed"
>> in v6_beta (with more irregularities near pial surface)
>> than in v5.3 according to coronal views of segmentations joined.
>>
>> What do you think about it ?  Would you advise me to go on with the
>> v6_beta anyway ?
>>
>> Would it be better and coherent to use a more recent "nightly dev builds"
>> of FreeSurfer for future publication ?
>>
>> Thanks in advance for helping !
>>
>> Best regards,
>>
>> Matthieu
>>
>> 2015-12-15 17:38 GMT+01:00 Bruce Fischl :
>>   Hi Matthieu
>>
>>   I think 6.0 looks better overall, even in the beta that you have.
>> The 5.3
>>   segmentation looks like it is underestimating cerebellum and
>> hippocampus to
>>   me.
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:
>>
>>   > Dear FS's experts,
>>   >
>>   > I have tried the recon-all process on one subject with both FS
>> v5.3 and v6_beta.
>>   >
>>   > Although subcortical structures seems to be better segmented in
>> v6_beta, I find that v6_beta over-segmented some
>>   other
>>   > structures as cerebellum, hippocampus, ...
>>   >
>>   > I will attached in the FileDrop my T1.mgz, and
>> aparc.a2009s+aseg.mgz files for both freesurfer versions.
>>   >
>>   > Could you please look at it and tell me what do you think about
>> and advise me ?
>>   >
>>   > Thank you !
>>   >
>>   > Best regards,
>>   > Matthieu
>>   >
>>   >
>> ___
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>>
>>
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
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>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] Segmentation comparison between FS5.3 and FS6beta

[Matthieu Vanhoutte]

Sorry Douglas I didn't well understand what you mean. Did you mean that
results from beta distribution aren't valuable ?

Best regards,

Matthieu
Le 15 déc. 2015 19:24, "Douglas N Greve"  a
écrit :

> btw, we are still making changes to version 6 so don't assume that the
> results from the beta will be consistent with the current beta
> distribution.
>
> On 12/15/2015 12:22 PM, Bruce Fischl wrote:
> > Hi Matthiew
> >
> > we are still hoping to get an official v6 release out in the next
> > month or two, so it would be best to use that which I think will
> > outperform whatever beta you have and 5.3. If you can't wait you are
> > probably better off using 5.3 (although I think the v6 you have is
> > more  accurate) so that people can at least replicate the software
> > version you are using
> >
> > cheers
> > Bruce
> >
> > On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:
> >
> >> Hi Bruce,
> >>
> >> Is it better to overestimate than underestimate ? Please find joined
> >> this two saggital images (FS v5.3 and FS v6_beta) of brain
> >> segmentation. Cerebellum in v6_beta really seems to go outside of its
> >> borderlines even if cerebellum in v5.3 is indeed lightly
> >> underestimated.
> >>
> >> Looking at the cerebral cortex I found the segmentation less
> >> "smoothed" in v6_beta (with more irregularities near pial surface)
> >> than in v5.3 according to coronal views of segmentations joined.
> >>
> >> What do you think about it ?  Would you advise me to go on with the
> >> v6_beta anyway ?
> >>
> >> Would it be better and coherent to use a more recent "nightly dev
> >> builds" of FreeSurfer for future publication ?
> >>
> >> Thanks in advance for helping !
> >>
> >> Best regards,
> >>
> >> Matthieu
> >>
> >> 2015-12-15 17:38 GMT+01:00 Bruce Fischl :
> >>   Hi Matthieu
> >>
> >>   I think 6.0 looks better overall, even in the beta that you
> >> have. The 5.3
> >>   segmentation looks like it is underestimating cerebellum and
> >> hippocampus to
> >>   me.
> >>
> >>   cheers
> >>   Bruce
> >>
> >>
> >>   On Tue, 15 Dec 2015, Matthieu Vanhoutte wrote:
> >>
> >>   > Dear FS's experts,
> >>   >
> >>   > I have tried the recon-all process on one subject with both
> >> FS v5.3 and v6_beta.
> >>   >
> >>   > Although subcortical structures seems to be better segmented
> >> in v6_beta, I find that v6_beta over-segmented some
> >>   other
> >>   > structures as cerebellum, hippocampus, ...
> >>   >
> >>   > I will attached in the FileDrop my T1.mgz, and
> >> aparc.a2009s+aseg.mgz files for both freesurfer versions.
> >>   >
> >>   > Could you please look at it and tell me what do you think
> >> about and advise me ?
> >>   >
> >>   > Thank you !
> >>   >
> >>   > Best regards,
> >>   > Matthieu
> >>   >
> >>   >
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> The information in this e-mail is intended only for the person to
> >> whom it is
> >> addressed. If you believe this e-mail was sent to you in error and
> >> the e-mail
> >> contains patient information, please contact the Partners Compliance
> >> HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to
> >> you in error
> >> but does not contain patient information, please contact the sender
> >> and properly
> >> dispose of the e-mail.
> >>
> >>
> >>
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Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Matthieu Vanhoutte]

Thanks Douglas for the answer !

But isn't PVC design for better working in terms of results with v6_beta
than v5.3 ?

Best regards,

Matthieu
Le 15 déc. 2015 19:02, "Douglas N Greve"  a
écrit :

> It is not subsegmented in 6.0 either:). When you run gtmseg, it will
> create the new segmentation that include pons and a few other things
>
> On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > Please see below :
> >
> > 2015-12-15 18:37 GMT+01:00 Douglas N Greve  > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> >
> >
> > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> > > Dear experts,
> > >
> > > Could anyone answer to my questions below ?
> > >
> > > Thanks !
> > >
> > > Best regards,
> > > Matthieu
> > >
> > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
> > >  > <mailto:matthieuvanhou...@gmail.com>
> > <mailto:matthieuvanhou...@gmail.com
> > <mailto:matthieuvanhou...@gmail.com>>>:
> > >
> > > Dear FS experts,
> > >
> > > 1) First Is it possible to use the partial volume correction
> > > provided in the v6 beta version of FreeSurfer despite the fact
> > > that recon-all have been done for all subjects with the v5.3 ?
> > >
> > Yes
> >
> >
> > Great ! but isn't it a problem for computing rSUV with pons as
> > reference structure since brainstem isn't sub-segmented in the version
> > 5.3 of recon-all ?
> >
> > >
> > >
> > > 2) Does this method supply an intensity normalisation for
> > PET images ?
> > >
> > What do you mean by intensity normalization? For uptake analysis,
> > people
> > usually use SUV (standard uptake values where the whole image is
> > scaled
> > by a value related to the injection mass and subject weight) or you
> > choose a reference structure to scale by (often called rSUV for
> > relative). By default mri_gtmpvc uses pons, but you can choose any
> > structure you want with the --rescale flag
> >
> > >
> > >
> > > Best regards,
> > > Matthieu
> > >
> > >
> > >
> > >
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> >
> > --
> >
> >
> > Best regards,
> > Matthieu
> >
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
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> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-7