[Freesurfer] ATTACHMENT REMOVED--Re: lGI ?h.pial-outer-smoothed

[Stripeikyte, G.]

Hi Marie,

Freesurfer version is:  freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0; 
Matlab version: 7.9.0 (R2009b).
Also when I open matlab I get warning that:

Warning: glibc 2.3.4  - Your version

 glibc 2.3.6  - MATLAB built using this version

I have attached recon-all.log file and pial surface screenshots


Thanks for your time!

Best,

Giedre

From: Marie Schaer mailto:marie.sch...@unige.ch>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday 4 March 2015 20:50
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] lGI ?h.pial-outer-smoothed


Hi Giedre,

Can you send me just the pial surface of this subject, and the recon-all.log 
(in the scripts folder) and I'll have a look. Please also let me know which 
version of freesurfer you are running, and which matlab version.

Best,

Marie

On Mar 4, 2015, at 3:08 AM, "Stripeikyte, G." 
mailto:g.stripeik...@umcutrecht.nl>>
 wrote:

Hi Marie,

Thanks for advice. I  have attached a screenshot of overlaid lGI.  I have at 
least 4 subjects with extremely high values of total 106.

Best,
Giedre

From: Marie Schaer mailto:marie.sch...@unige.ch>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday 3 March 2015 21:00
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] lGI ?h.pial-outer-smoothed


Hi Giedre,

Small intersections like that are fine and won't affect the lGI computation, so 
you are good with that. Values around 20 are however more preoccupying! Can you 
send me a screenshot of the lGI overlaid on the surface for this subject using 
tksurfer or freeview?

Best,

Marie

NB: if you are interested in thickness as well, you might want to correct the 
segmentation in the parahippocampal gyrus for this subject (the "drop-shaped" 
WM inclusion in the cortex).

On Mar 3, 2015, at 6:58 AM, "Stripeikyte, G." 
mailto:g.stripeik...@umcutrecht.nl>> wrote:

Dear freesurfers,

I am analysing localGI and noticed that sometimes scans with 
?h.pial-outer-smoothed surface intersect ?h.pial surface (attached pic.). Is 
this normal or  should I correct parameters and rerun localGI? Also when I 
extracted ROI lGI values I got some extremely high results. For example in 
lh_insula and rh_insula, for some participants lGI reach about 20. Scans look 
normal of these participants. Are such high values possible or something wrong 
with calculation?

Sincerely,
Giedre


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Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

[Krieger, Donald N.]

Glad it helped, Zack.
It’s such a pleasure to come across something I understand.

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Zachary Greenberg
Sent: Wednesday, March 04, 2015 7:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

awesome! thanks a bunch Don.


-zack

On Wed, Mar 4, 2015 at 4:24 PM, Krieger, Donald N. 
mailto:krieg...@upmc.edu>> wrote:
Hi Zack,

It looks like mris_info send that matrix out on the error output rather than 
the standard output.
I just tried it and you can get it by redirecting both to your file like this:
Try  mris_info lh.pial >& lh_info.txt

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu]
 On Behalf Of Zachary Greenberg
Sent: Wednesday, March 04, 2015 7:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

Thanks bruce. It will work out fine if I can just pull out that c_(ras) array 
in a pipelined way to apply it to the ascii data.

I'm struggling a bit to achieve that though. I think because mris_info outputs 
the tables of *_(ras) info in a strange way. For example, if I try to cat the 
output of mris_info to a txt file: 'mris_info lh.pial > lh_info.txt', the text 
file will contain everything except the *_(ras) info table that you see if you 
just call the command by itself:


volume geometry:

extent  : (256, 256, 256)

voxel   : ( 1.,  1.,  1.)

x_(ras) : (-1.,  0.,  0.)

y_(ras) : ( 0.,  0., -1.)

z_(ras) : ( 0.,  1.,  0.)

c_(ras) : (-1.6000, -5.1750, -15.3313)

file: ../mri/filled-pretess255.mgz



Are there any mris_info experts on the team who might know how to circumvent 
this?



thanks again for your help!

-zack

On Wed, Mar 4, 2015 at 2:54 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Zack

the ascii format I don't think supports the c_ras info, which is why you see a 
shift

cheers
Bruce

On Wed, 4 Mar 2015, Zachary Greenberg wrote:
Ok I figured out that this shift corresponds to the c_(RAS) value in the
header of lh.pial, which you can get with 'mris_info lh.pial'
Alternatively you can get the first coordinate and subtract it from the
first coordinate of lh.pial.asc with 'mris_info lh.pial --v 0'

Is there a way I'm not thinking of to output c_(RAS) directly using
mris_info or a bash command (cat grep)?

Thanks again,

-zack

On Wed, Mar 4, 2015 at 12:54 PM, Zachary Greenberg
mailto:zacharyigreenb...@gmail.com>> wrote:
  Hi all,
I discovered that converting the mesh data from freesurfer lh.pial
format to ascii (.asc) causes a shift in the coordinates of the mesh.
You can see this by overlaying the two surfaces in freeview, and
looking at the difference between the [0 0 0] surface RAS coordinate
in lh.pial vs lh.pial.asc.

The shift is not consistent across different subjects. I'm wondering
if there is a way to fix this, or if there is some regularity in the
coordinate shift that can be used to correct (that I'm not seeing).

For example the difference coordinates between lh.pial and lh.pial.asc
in two different subjects are:
[  1.6 ,   5.18,  15.33]
[2.02, -15.80, 0.18]


Thanks for any help you can offer!

-zack








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--
Zachary Greenberg
Imaging Specialist
Department of Neurological Surgery
University of California, San Francisco
Email: 
Zachary.greenb...@ucsf.edu



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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  > >:
> >
> >
> > 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
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu   Freesurfer@nmr.mgh.harvard.edu>
> >> https://mail

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 > > >:
>> >
>> >
>> > 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 

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

[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  >:
>
>
> 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
> >>

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

[Douglas N Greve]

Also, you can do everything in one vol2surf command with --trgsubject 
fsaverage. It is identical to doing it in two steps
On 03/05/2015 08:12 AM, Matthieu Vanhoutte wrote:
> *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 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/
>
>
> (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 
> mailto:matthieuvanhou...@gmail.com>>:
>
> 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>
> > 

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  > >:
> >
> >
> > 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 --

Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

[Douglas N Greve]

You can also get the cras from

mri_info --cras orig.mgz





On 03/04/2015 07:35 PM, Bruce Fischl wrote:
> hmmm, not sure why. If this is a problem we can certainly change it, 
> just let us know
> On Thu, 5 Mar 2015, Krieger, Donald N. wrote:
>
>>
>> Hi Zack,
>>
>>
>>
>> It looks like mris_info send that matrix out on the error output 
>> rather than
>> the standard output.
>>
>> I just tried it and you can get it by redirecting both to your file like
>> this:
>>
>> Try  mris_info lh.pial >& lh_info.txt
>>
>>
>>
>> Regards,
>>
>>
>>
>> Don
>>
>>
>>
>> Signature0001
>>
>> Don Krieger, Ph.D.
>>
>> Department of Neurological Surgery
>>
>> University of Pittsburgh
>>
>>
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Zachary
>> Greenberg
>> Sent: Wednesday, March 04, 2015 7:05 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate
>> shift
>>
>>
>>
>> Thanks bruce. It will work out fine if I can just pull out that c_(ras)
>> array in a pipelined way to apply it to the ascii data.
>>
>>
>>
>> I'm struggling a bit to achieve that though. I think because mris_info
>> outputs the tables of *_(ras) info in a strange way. For example, if 
>> I try
>> to cat the output of mris_info to a txt file: 'mris_info lh.pial >
>> lh_info.txt', the text file will contain everything except the 
>> *_(ras) info
>> table that you see if you just call the command by itself:
>>
>>
>>
>> volume geometry:
>>
>> extent  : (256, 256, 256)
>>
>> voxel   : ( 1.,  1.,  1.)
>>
>> x_(ras) : (-1.,  0.,  0.)
>>
>> y_(ras) : ( 0.,  0., -1.)
>>
>> z_(ras) : ( 0.,  1.,  0.)
>>
>> c_(ras) : (-1.6000, -5.1750, -15.3313)
>>
>> file: ../mri/filled-pretess255.mgz
>>
>>
>>
>> Are there any mris_info experts on the team who might know how to 
>> circumvent
>> this?
>>
>>
>>
>> thanks again for your help!
>>
>> -zack
>>
>>
>>
>> On Wed, Mar 4, 2015 at 2:54 PM, Bruce Fischl 
>> 
>> wrote:
>>
>> Hi Zack
>>
>> the ascii format I don't think supports the c_ras info, which is why 
>> you see
>> a shift
>>
>> cheers
>> Bruce
>>
>>
>> On Wed, 4 Mar 2015, Zachary Greenberg wrote:
>>
>> Ok I figured out that this shift corresponds to the c_(RAS) value in the
>> header of lh.pial, which you can get with 'mris_info lh.pial'
>> Alternatively you can get the first coordinate and subtract it from the
>> first coordinate of lh.pial.asc with 'mris_info lh.pial --v 0'
>>
>> Is there a way I'm not thinking of to output c_(RAS) directly using
>> mris_info or a bash command (cat grep)?
>>
>> Thanks again,
>>
>> -zack
>>
>> On Wed, Mar 4, 2015 at 12:54 PM, Zachary Greenberg
>>  wrote:
>>   Hi all,
>> I discovered that converting the mesh data from freesurfer lh.pial
>> format to ascii (.asc) causes a shift in the coordinates of the mesh.
>> You can see this by overlaying the two surfaces in freeview, and
>> looking at the difference between the [0 0 0] surface RAS coordinate
>> in lh.pial vs lh.pial.asc.
>>
>> The shift is not consistent across different subjects. I'm wondering
>> if there is a way to fix this, or if there is some regularity in the
>> coordinate shift that can be used to correct (that I'm not seeing).
>>
>> For example the difference coordinates between lh.pial and lh.pial.asc
>> in two different subjects are:
>> [  1.6 ,   5.18,  15.33]
>> [2.02, -15.80, 0.18]
>>
>>
>> Thanks for any help you can offer!
>>
>> -zack
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> 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.
>>
>>
>>
>>
>>
>> -- 
>>
>> Zachary Greenberg
>>
>> Imaging Specialist
>>
>> Department of Neurological Surgery
>>
>> University of California, San Francisco
>>
>> Email: zachary.greenb...@ucsf.edu
>>
>>
>>
>>
>>
>>
>>
>
>
> ___
> 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

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

[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  >:
>
>
>
> #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
> >  
> >
> > >  
> >   > >
> > >
> > > 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). Wher

Re: [Freesurfer] Recon-all (Data for test )

[Z K]

https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data

!!!

-Zeke

On 03/05/2015 01:35 AM, Hassan bakhshi wrote:
> Hi
>
> Where can i find data to test freesurfer
>
> I want to test recon-all command and then get volume of hippocamp!!
>
> Thanks alot
>
>
> ___
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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  > >:
> >
> >
> >
> > #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

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

[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  >:
>
>
> 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
> >  
> >
> > >  
> >   > >
> > >
> > > On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> > > > Dear Doug,
> > > >
> > > > Thank you for helping !
> > > >
> > > > Yes I directly u

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  > >:
> >
> >
> > 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

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

[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  >:
>
> 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
> >  
> >
> > >  
> >   > >
> > >
> > >
> > > #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.f

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  > >:
> >
> > 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
> > >  > 
> >  >>
> > > >  > 
> > >  >  > > >
> > > >
> > > >
> > > > #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 pa

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

[Douglas N Greve]

The icoorder is only needed if you don't have a target subject.

To do your group analysis, you can just run mri_concat, eg,

mri_concat subject1/lh.fwhm3.fsaverage.cbf.mgh 
subject2/lh.fwhm3.fsaverage.cbf.mgh --o 
all.subjects.lh.fwhm3.fsaverage.cbf.mgh

Then use all.subjects.lh.fwhm3.fsaverage.cbf.mgh as input to mri_glmfit




On 03/05/2015 12:16 PM, Matthieu Vanhoutte wrote:
> 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
> >  
> >
> > >  
> >   > >
> > >
> > > 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
> > >  
> >  >
> >  
> >>
> > > >

[Freesurfer] use of info from cortical parcellation in TRACULA

[Janosch Linkersdörfer]

Hi Anastasia and others,

I am sorry if I just did a bad job, but I could not find information on how 
information from the cortical parcellation is used in the path tracking done by 
TRACULA, especially, which cortical labels are used as determinants (seed, 
waypoint) for which tracts.

It would be great if you could point me in the right direction!

Thanks a lot,

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

[Douglas N Greve]

Yes. You don't want to sample at the white because you'll get large 
partial volume effects. The mid is better. Having said that, I don't see 
large differences in fMRI at typical voxel sizes ~3mm

doug

On 03/05/2015 12:27 PM, Matthieu Vanhoutte wrote:
> Many thanks Doug !
>
> Last point of vue concerning the command : is the --surf mid (mean 
> surface between pial and white) better than default white ?
>
> /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o 
> //lh.fwhm3.fsaverage.cbf.mgh --regheader ///subj_id/ --surf-fwhm 3/ 
> --trgsubject fsaverage --cortex
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-03-05 18:23 GMT+01:00 Douglas N Greve  >:
>
>
> The icoorder is only needed if you don't have a target subject.
>
> To do your group analysis, you can just run mri_concat, eg,
>
> mri_concat subject1/lh.fwhm3.fsaverage.cbf.mgh
> subject2/lh.fwhm3.fsaverage.cbf.mgh --o
> all.subjects.lh.fwhm3.fsaverage.cbf.mgh
>
> Then use all.subjects.lh.fwhm3.fsaverage.cbf.mgh as input to
> mri_glmfit
>
>
>
>
> On 03/05/2015 12:16 PM, Matthieu Vanhoutte wrote:
> > 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
> mailto:gr...@nmr.mgh.harvard.edu>
> >  >>:
> >
> > 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
> >  
> >
> > >  
> >   > >
> > > 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

[Freesurfer] using custom templates

[Jason Tourville]

Greetings,
I have generated custom surface templates from pediatric data sets. To
apply it to the larger data set, is it sufficient to simply run the
autorecon3 steps (perhaps skipping the mris_sphere step)? If so, is there a
handy flag for running this with recon-all and/or a way to run autorecon3
with a flag indicating that the non-default template should be used?

Once I've done this, I'd like to do some form of comparison b/w the
templates. I am considering looking at the overlap of surface labels
generated by the custom templates to a manually labeled "gold standard."
Does that sound reasonable? Do you have any other suggestions?

Best,
Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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Re: [Freesurfer] using custom templates

[Bruce Fischl]

Hi Jason

I don't think so - you'll probably have to edit the recon-all script. And 
by template do you just mean the folding pattern .tif files, or do you 
meant the parcellation atlases (*.gcs)?

cheers
Bruce
On Thu, 5 Mar 2015, Jason Tourville 
wrote:

> Greetings,
> I have generated custom surface templates from pediatric data sets. To apply
> it to the larger data set, is it sufficient to simply run the autorecon3
> steps (perhaps skipping the mris_sphere step)? If so, is there a handy flag
> for running this with recon-all and/or a way to run autorecon3 with a flag
> indicating that the non-default template should be used?
> 
> Once I've done this, I'd like to do some form of comparison b/w the
> templates. I am considering looking at the overlap of surface labels
> generated by the custom templates to a manually labeled "gold standard."
> Does that sound reasonable? Do you have any other suggestions?
> 
> Best,
> Jason
> 
> --
> Jason A. Tourville, Ph.D.
> Research Assistant Professor
> Department of Speech, Language,
> and Hearing Sciences
> Boston University
> 677 Beacon St.
> Boston, MA 02215
> Phone: (617)353-9484
> Fax: (617)353-7755
> 
>
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Re: [Freesurfer] using custom templates

[Douglas N Greve]

If you used make_average_subject to create the template, you can run 
surfreg to do the registration. If/when you run mris_preproc, make sure 
to spec both the target subject and the new spherical registration


On 03/05/2015 03:18 PM, Bruce Fischl wrote:
> Hi Jason
>
> I don't think so - you'll probably have to edit the recon-all script. And
> by template do you just mean the folding pattern .tif files, or do you
> meant the parcellation atlases (*.gcs)?
>
> cheers
> Bruce
> On Thu, 5 Mar 2015, Jason Tourville
> wrote:
>
>> Greetings,
>> I have generated custom surface templates from pediatric data sets. To apply
>> it to the larger data set, is it sufficient to simply run the autorecon3
>> steps (perhaps skipping the mris_sphere step)? If so, is there a handy flag
>> for running this with recon-all and/or a way to run autorecon3 with a flag
>> indicating that the non-default template should be used?
>>
>> Once I've done this, I'd like to do some form of comparison b/w the
>> templates. I am considering looking at the overlap of surface labels
>> generated by the custom templates to a manually labeled "gold standard."
>> Does that sound reasonable? Do you have any other suggestions?
>>
>> Best,
>> Jason
>>
>> --
>> Jason A. Tourville, Ph.D.
>> Research Assistant Professor
>> Department of Speech, Language,
>> and Hearing Sciences
>> Boston University
>> 677 Beacon St.
>> Boston, MA 02215
>> Phone: (617)353-9484
>> Fax: (617)353-7755
>>
>>
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>
>

-- 
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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Re: [Freesurfer] using custom templates

[Jason Tourville]

Hi Bruce,
By template here, I mean the folding pattern .tif files. The intention is
to have  a replacement for the fsaverage template for surfer
co-registration.

Cheers,
Jason


On Thu, Mar 5, 2015 at 3:18 PM, Bruce Fischl 
wrote:

> Hi Jason
>
> I don't think so - you'll probably have to edit the recon-all script. And
> by template do you just mean the folding pattern .tif files, or do you
> meant the parcellation atlases (*.gcs)?
>
> cheers
> Bruce
> On Thu, 5 Mar 2015, Jason Tourville
> wrote:
>
> > Greetings,
> > I have generated custom surface templates from pediatric data sets. To
> apply
> > it to the larger data set, is it sufficient to simply run the autorecon3
> > steps (perhaps skipping the mris_sphere step)? If so, is there a handy
> flag
> > for running this with recon-all and/or a way to run autorecon3 with a
> flag
> > indicating that the non-default template should be used?
> >
> > Once I've done this, I'd like to do some form of comparison b/w the
> > templates. I am considering looking at the overlap of surface labels
> > generated by the custom templates to a manually labeled "gold standard."
> > Does that sound reasonable? Do you have any other suggestions?
> >
> > Best,
> > Jason
> >
> > --
> > Jason A. Tourville, Ph.D.
> > Research Assistant Professor
> > Department of Speech, Language,
> > and Hearing Sciences
> > Boston University
> > 677 Beacon St.
> > Boston, MA 02215
> > Phone: (617)353-9484
> > Fax: (617)353-7755
> >
> >
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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.
>
>


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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Re: [Freesurfer] using custom templates

[Jason Tourville]

Hi Doug,
I've run the steps outlined in the SurfaceRegAndTemplates page so far. So:

make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ...

foreach subject (subj1 subj2 subj3 ...)
  cd $SUBJECTS_DIR/subject
  mris_register -curv surf/lh.sphere \
 $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
 surf/lh.sphere.reg.newtemplate
end

mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ...

make_average_subject --out newnewtemplate --surf-reg
sphere.reg.newtemplate \
  --subjects subj1 subj2 subj3 ...

My understanding is that the next step is to now register each individual
surface to this new template and then run through the surface (and volume)
labeling steps. Is that correct?

It occurs to me that the fsaverage template used as the target for any .gcs
that I would to label the surface. Will I have to account for this?

Thanks again,
Jason




On Thu, Mar 5, 2015 at 3:26 PM, Douglas N Greve 
wrote:

>
> If you used make_average_subject to create the template, you can run
> surfreg to do the registration. If/when you run mris_preproc, make sure
> to spec both the target subject and the new spherical registration
>
>
> On 03/05/2015 03:18 PM, Bruce Fischl wrote:
> > Hi Jason
> >
> > I don't think so - you'll probably have to edit the recon-all script. And
> > by template do you just mean the folding pattern .tif files, or do you
> > meant the parcellation atlases (*.gcs)?
> >
> > cheers
> > Bruce
> > On Thu, 5 Mar 2015, Jason Tourville
> > wrote:
> >
> >> Greetings,
> >> I have generated custom surface templates from pediatric data sets. To
> apply
> >> it to the larger data set, is it sufficient to simply run the autorecon3
> >> steps (perhaps skipping the mris_sphere step)? If so, is there a handy
> flag
> >> for running this with recon-all and/or a way to run autorecon3 with a
> flag
> >> indicating that the non-default template should be used?
> >>
> >> Once I've done this, I'd like to do some form of comparison b/w the
> >> templates. I am considering looking at the overlap of surface labels
> >> generated by the custom templates to a manually labeled "gold standard."
> >> Does that sound reasonable? Do you have any other suggestions?
> >>
> >> Best,
> >> Jason
> >>
> >> --
> >> Jason A. Tourville, Ph.D.
> >> Research Assistant Professor
> >> Department of Speech, Language,
> >> and Hearing Sciences
> >> Boston University
> >> 677 Beacon St.
> >> Boston, MA 02215
> >> Phone: (617)353-9484
> >> Fax: (617)353-7755
> >>
> >>
> > ___
> > 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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>


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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Re: [Freesurfer] Expediting the pial surface calculation

[Borzello, Mia]

I'm having the same issue- any updates on this problem that Jason Naftulin 
posted?

Thanks,
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Naftulin, Jason Scott
Sent: Friday, February 27, 2015 2:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Expediting the pial surface calculation

Hi,

We are wondering if there is a faster way to generate lh.pial and rh.pial than 
running the 24 hour long recon-all function. We took a look at 
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps  and it seems 
that the inputs for lh.pial and rh.pial are needed from the recon-all output. 
We were wondering how difficult it would be to generate a custom script to 
significantly decrease the amount of time needed to generate these two 
surfaces. Is there someone we can talk to who might be interested in doing this?

Also, we are wondering if there is an object in Freesurfer that handles the 
entire brain as one object instead of as two separate hemispheres. We would 
like to 3D print the entire brain at once with accurate inter-hemisphere 
relationship.

Any and all advice you can provide would be most helpful.


Thanks,
Jason
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Re: [Freesurfer] using custom templates

[Douglas N Greve]

The mris_register command is what does the registration and creates a 
new sphere.reg file. surfreg just implements that command mris_register 
command.

I'm not sure what you mean by the labeling steps.


On 03/05/2015 03:53 PM, Jason Tourville wrote:
> Hi Doug,
> I've run the steps outlined in the SurfaceRegAndTemplates page so far. So:
> make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ...
>
> foreach subject (subj1 subj2 subj3 ...)
>cd $SUBJECTS_DIR/subject
>mris_register -curv surf/lh.sphere \
>   $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
>   surf/lh.sphere.reg.newtemplate
> end
>
> mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 
> ...
>
> make_average_subject --out newnewtemplate --surf-reg
> sphere.reg.newtemplate \
>--subjects subj1 subj2 subj3 ...
>
> My understanding is that the next step is to now register each 
> individual surface to this new template and then run through the 
> surface (and volume) labeling steps. Is that correct?
>
> It occurs to me that the fsaverage template used as the target for any 
> .gcs that I would to label the surface. Will I have to account for this?
>
> Thanks again,
> Jason
>
>
>
>
> On Thu, Mar 5, 2015 at 3:26 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> If you used make_average_subject to create the template, you can run
> surfreg to do the registration. If/when you run mris_preproc, make
> sure
> to spec both the target subject and the new spherical registration
>
>
> On 03/05/2015 03:18 PM, Bruce Fischl wrote:
> > Hi Jason
> >
> > I don't think so - you'll probably have to edit the recon-all
> script. And
> > by template do you just mean the folding pattern .tif files, or
> do you
> > meant the parcellation atlases (*.gcs)?
> >
> > cheers
> > Bruce
> > On Thu, 5 Mar 2015, Jason Tourville
> > wrote:
> >
> >> Greetings,
> >> I have generated custom surface templates from pediatric data
> sets. To apply
> >> it to the larger data set, is it sufficient to simply run the
> autorecon3
> >> steps (perhaps skipping the mris_sphere step)? If so, is there
> a handy flag
> >> for running this with recon-all and/or a way to run autorecon3
> with a flag
> >> indicating that the non-default template should be used?
> >>
> >> Once I've done this, I'd like to do some form of comparison b/w the
> >> templates. I am considering looking at the overlap of surface
> labels
> >> generated by the custom templates to a manually labeled "gold
> standard."
> >> Does that sound reasonable? Do you have any other suggestions?
> >>
> >> Best,
> >> Jason
> >>
> >> --
> >> Jason A. Tourville, Ph.D.
> >> Research Assistant Professor
> >> Department of Speech, Language,
> >> and Hearing Sciences
> >> Boston University
> >> 677 Beacon St.
> >> Boston, MA 02215
> >> Phone: (617)353-9484 
> >> Fax: (617)353-7755 
> >>
> >>
> > ___
> > 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.
>
>
>
>
> -- 
> Jason A. Tourville, Ph.D.
> Research Assistant Professor
> Department of Speech, Language,
> and Hearing Sciences
> Boston University
> 677 Beacon St.
> Boston, MA 02215
> Phone: (617)353-9484
> Fax: (617)353-7755
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https

Re: [Freesurfer] Expediting the pial surface calculation

[Bruce Fischl]

sorry, the answer is pretty much "no" to both questions. We have 3D-printed 
surface models, but the steps for doing so aren't documented or supported. 
I guess the easiest thing to do would be to combine the surfaces in matlab. 
You'll have to add the # of vertices in one hemi to all the indices in the 
other (so that the indices remain unique, then concatenate them into a 
single surface tesselation and write it out


On Thu, 5 Mar 2015, 
Borzello, Mia wrote:



I'm having the same issue- any updates on this problem that Jason Naftulin
posted?
Thanks, 
m


From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Naftulin, Jason Scott
Sent: Friday, February 27, 2015 2:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Expediting the pial surface calculation

Hi,

We are wondering if there is a faster way to generate lh.pial and rh.pial
than running the 24 hour long recon-all function. We took a look
at http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps  and it
seems that the inputs for lh.pial and rh.pial are needed from the recon-all
output. We were wondering how difficult it would be to generate a custom
script to significantly decrease the amount of time needed to generate these
two surfaces. Is there someone we can talk to who might be interested in
doing this?

Also, we are wondering if there is an object in Freesurfer that handles the
entire brain as one object instead of as two separate hemispheres. We would
like to 3D print the entire brain at once
with accurate inter-hemisphere relationship.

Any and all advice you can provide would be most helpful.


Thanks,
Jason

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Re: [Freesurfer] Expediting the pial surface calculation

[Borzello, Mia]

Great- thanks for the quick reply!

m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, March 05, 2015 4:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Expediting the pial surface calculation

sorry, the answer is pretty much "no" to both questions. We have 3D-printed
surface models, but the steps for doing so aren't documented or supported.
I guess the easiest thing to do would be to combine the surfaces in matlab.
You'll have to add the # of vertices in one hemi to all the indices in the
other (so that the indices remain unique, then concatenate them into a
single surface tesselation and write it out

On Thu, 5 Mar 2015,
Borzello, Mia wrote:

> I'm having the same issue- any updates on this problem that Jason Naftulin
> posted?
> Thanks,
> m
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Naftulin, Jason Scott
> Sent: Friday, February 27, 2015 2:50 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Expediting the pial surface calculation
>
> Hi,
>
> We are wondering if there is a faster way to generate lh.pial and rh.pial
> than running the 24 hour long recon-all function. We took a look
> at http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps  and it
> seems that the inputs for lh.pial and rh.pial are needed from the recon-all
> output. We were wondering how difficult it would be to generate a custom
> script to significantly decrease the amount of time needed to generate these
> two surfaces. Is there someone we can talk to who might be interested in
> doing this?
>
> Also, we are wondering if there is an object in Freesurfer that handles the
> entire brain as one object instead of as two separate hemispheres. We would
> like to 3D print the entire brain at once
> with accurate inter-hemisphere relationship.
>
> Any and all advice you can provide would be most helpful.
>
>
> Thanks,
> Jason
>
>

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[Freesurfer] error with asegstats2table

[Maria Kharitonova]

Hi all,

I'm trying to extract aseg and aparc stats. Aparc worked fine, but when I'm 
trying to extract aseg stats, I get the following warnings, then error:

Parsing the .stats files
WARN: 3696 nmeasures = 66, expecting 55
WARN: 4455 nmeasures = 66, expecting 55
Building the table..
ERROR: All stat files should have the same segmentations
If one or more stats file have different segs from others,
use --common-segs or --all-segs flag depending on the need.

If I use the -all-segs flag like it suggests, I end up with 0s in the following 
variables: BrainSegVol BrainSegVolNotVent BrainSegVolNotVentSurf 
SupraTentorialVolNotVent SupraTentorialVolNotVentVox MaskVol 
BrainSegVol-to-eTIV MaskVol-to-eTIV lhSurfaceHoles rhSurfaceHoles SurfaceHoles 
EstimatedTotalIntraCranialVol

I've run this command before and never ran into this issue. Do you have any 
ideas for how to extract the necessary volume information without errors?

Thanks,
Maria

--
Maria Kharitonova, PhD
Research Assistant Professor
Department of Medical Social Sciences
Northwestern University Feinberg School of Medicine
625 N. Michigan Ave, Suite 2700
Chicago, IL 60611
Phone: (312) 503-6503
Email: maria.khariton...@northwestern.edu

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Re: [Freesurfer] error with asegstats2table

[Douglas N Greve]

Did you run different subjects with different version of freesurfer (or 
with different version of mri_segstats)?

On 03/05/2015 04:26 PM, Maria Kharitonova wrote:
> Hi all,
>
> I’m trying to extract aseg and aparc stats. Aparc worked fine, but 
> when I’m trying to extract aseg stats, I get the following warnings, 
> then error:
>
> Parsing the .stats files
> WARN: 3696 nmeasures = 66, expecting 55
> WARN: 4455 nmeasures = 66, expecting 55
> Building the table..
> ERROR: All stat files should have the same segmentations
> If one or more stats file have different segs from others,
> use --common-segs or --all-segs flag depending on the need.
>
> If I use the —all-segs flag like it suggests, I end up with 0s in the 
> following variables: 
> BrainSegVolBrainSegVolNotVentBrainSegVolNotVentSurfSupraTentorialVolNotVentSupraTentorialVolNotVentVoxMaskVolBrainSegVol-to-eTIVMaskVol-to-eTIVlhSurfaceHolesrhSurfaceHolesSurfaceHolesEstimatedTotalIntraCranialVol
>
> I’ve run this command before and never ran into this issue. Do you 
> have any ideas for how to extract the necessary volume information 
> without errors?
>
> Thanks,
> Maria
>
> --
> Maria Kharitonova, PhD
> Research Assistant Professor
> Department of Medical Social Sciences
> Northwestern University Feinberg School of Medicine
> 625 N. Michigan Ave, Suite 2700
> Chicago, IL 60611
> Phone: (312) 503-6503
> Email: maria.khariton...@northwestern.edu
>
>
>
> ___
> 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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Re: [Freesurfer] using custom templates

[Jason Tourville]

Hi Doug,
Perhaps I should back up and explain our goal. We are using Freesurfer to
recon pediatric data sets and are planning to use the surface labels as
seeds for connectivity studies and for morphometric analyses. We're
concerned that using the fsaverage surface template as the target for
surface registration could introduce errors in the labels due to match with
our pediatric surfaces, so we derived a new surface template from a subset
of our data set.

My understanding is that once we've done this, to get the surface labels,
stats, etc. for each scan, we need to then register each scan to this new
target and then run the the various steps to get the labeled surfaces
(e.g., mris_ca_label). So I want to confirm this; more specifically, I'd
like to know which steps of the recon-all pipeline need to be rerun to to
replace completely replace the fsaverage target.

Jason


On Thu, Mar 5, 2015 at 3:58 PM, Douglas N Greve 
wrote:

> The mris_register command is what does the registration and creates a
> new sphere.reg file. surfreg just implements that command mris_register
> command.
>
> I'm not sure what you mean by the labeling steps.
>
>
> On 03/05/2015 03:53 PM, Jason Tourville wrote:
> > Hi Doug,
> > I've run the steps outlined in the SurfaceRegAndTemplates page so far.
> So:
> > make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ...
> >
> > foreach subject (subj1 subj2 subj3 ...)
> >cd $SUBJECTS_DIR/subject
> >mris_register -curv surf/lh.sphere \
> >   $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
> >   surf/lh.sphere.reg.newtemplate
> > end
> >
> > mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s
> subj3 ...
> >
> > make_average_subject --out newnewtemplate --surf-reg
> > sphere.reg.newtemplate \
> >--subjects subj1 subj2 subj3 ...
> >
> > My understanding is that the next step is to now register each
> > individual surface to this new template and then run through the
> > surface (and volume) labeling steps. Is that correct?
> >
> > It occurs to me that the fsaverage template used as the target for any
> > .gcs that I would to label the surface. Will I have to account for this?
> >
> > Thanks again,
> > Jason
> >
> >
> >
> >
> > On Thu, Mar 5, 2015 at 3:26 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > If you used make_average_subject to create the template, you can run
> > surfreg to do the registration. If/when you run mris_preproc, make
> > sure
> > to spec both the target subject and the new spherical registration
> >
> >
> > On 03/05/2015 03:18 PM, Bruce Fischl wrote:
> > > Hi Jason
> > >
> > > I don't think so - you'll probably have to edit the recon-all
> > script. And
> > > by template do you just mean the folding pattern .tif files, or
> > do you
> > > meant the parcellation atlases (*.gcs)?
> > >
> > > cheers
> > > Bruce
> > > On Thu, 5 Mar 2015, Jason Tourville
> > > wrote:
> > >
> > >> Greetings,
> > >> I have generated custom surface templates from pediatric data
> > sets. To apply
> > >> it to the larger data set, is it sufficient to simply run the
> > autorecon3
> > >> steps (perhaps skipping the mris_sphere step)? If so, is there
> > a handy flag
> > >> for running this with recon-all and/or a way to run autorecon3
> > with a flag
> > >> indicating that the non-default template should be used?
> > >>
> > >> Once I've done this, I'd like to do some form of comparison b/w
> the
> > >> templates. I am considering looking at the overlap of surface
> > labels
> > >> generated by the custom templates to a manually labeled "gold
> > standard."
> > >> Does that sound reasonable? Do you have any other suggestions?
> > >>
> > >> Best,
> > >> Jason
> > >>
> > >> --
> > >> Jason A. Tourville, Ph.D.
> > >> Research Assistant Professor
> > >> Department of Speech, Language,
> > >> and Hearing Sciences
> > >> Boston University
> > >> 677 Beacon St.
> > >> Boston, MA 02215
> > >> Phone: (617)353-9484 
> > >> Fax: (617)353-7755 
> > >>
> > >>
> > > ___
> > > 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
> > 

Re: [Freesurfer] using custom templates

[Douglas N Greve]

I don't think this makes sense unless you have created a new label atlas 
for your individual subjects. The current label atlas exists in the 
fsaverage space. Maybe Bruce can weigh in.

On 03/05/2015 04:46 PM, Jason Tourville wrote:
> Hi Doug,
> Perhaps I should back up and explain our goal. We are using Freesurfer 
> to recon pediatric data sets and are planning to use the surface 
> labels as seeds for connectivity studies and for morphometric 
> analyses. We're concerned that using the fsaverage surface template as 
> the target for surface registration could introduce errors in the 
> labels due to match with our pediatric surfaces, so we derived a new 
> surface template from a subset of our data set.
>
> My understanding is that once we've done this, to get the surface 
> labels, stats, etc. for each scan, we need to then register each scan 
> to this new target and then run the the various steps to get the 
> labeled surfaces (e.g., mris_ca_label). So I want to confirm this; 
> more specifically, I'd like to know which steps of the recon-all 
> pipeline need to be rerun to to replace completely replace the 
> fsaverage target.
>
> Jason
>
>
> On Thu, Mar 5, 2015 at 3:58 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> The mris_register command is what does the registration and creates a
> new sphere.reg file. surfreg just implements that command
> mris_register
> command.
>
> I'm not sure what you mean by the labeling steps.
>
>
> On 03/05/2015 03:53 PM, Jason Tourville wrote:
> > Hi Doug,
> > I've run the steps outlined in the SurfaceRegAndTemplates page
> so far. So:
> > make_average_subject --out newtemplate --subjects subj1 subj2
> subj3 ...
> >
> > foreach subject (subj1 subj2 subj3 ...)
> >cd $SUBJECTS_DIR/subject
> >mris_register -curv surf/lh.sphere \
> >   $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
> >   surf/lh.sphere.reg.newtemplate
> > end
> >
> > mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s
> subj2 --s subj3 ...
> >
> > make_average_subject --out newnewtemplate --surf-reg
> > sphere.reg.newtemplate \
> >--subjects subj1 subj2 subj3 ...
> >
> > My understanding is that the next step is to now register each
> > individual surface to this new template and then run through the
> > surface (and volume) labeling steps. Is that correct?
> >
> > It occurs to me that the fsaverage template used as the target
> for any
> > .gcs that I would to label the surface. Will I have to account
> for this?
> >
> > Thanks again,
> > Jason
> >
> >
> >
> >
> > On Thu, Mar 5, 2015 at 3:26 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> >
> > If you used make_average_subject to create the template, you
> can run
> > surfreg to do the registration. If/when you run
> mris_preproc, make
> > sure
> > to spec both the target subject and the new spherical
> registration
> >
> >
> > On 03/05/2015 03:18 PM, Bruce Fischl wrote:
> > > Hi Jason
> > >
> > > I don't think so - you'll probably have to edit the recon-all
> > script. And
> > > by template do you just mean the folding pattern .tif
> files, or
> > do you
> > > meant the parcellation atlases (*.gcs)?
> > >
> > > cheers
> > > Bruce
> > > On Thu, 5 Mar 2015, Jason Tourville
> > > wrote:
> > >
> > >> Greetings,
> > >> I have generated custom surface templates from pediatric data
> > sets. To apply
> > >> it to the larger data set, is it sufficient to simply run the
> > autorecon3
> > >> steps (perhaps skipping the mris_sphere step)? If so, is
> there
> > a handy flag
> > >> for running this with recon-all and/or a way to run
> autorecon3
> > with a flag
> > >> indicating that the non-default template should be used?
> > >>
> > >> Once I've done this, I'd like to do some form of
> comparison b/w the
> > >> templates. I am considering looking at the overlap of surface
> > labels
> > >> generated by the custom templates to a manually labeled "gold
> > standard."
> > >> Does that sound reasonable? Do you have any other
> suggestions?
> > >>
> > >> Best,
> > >> Jason
> > >>
> > >> --
> > >> Jason A. Tourville, Ph.D.
> > >> Research Assistant Professor
> > >> Department of Speech, Language,
> > >> and Hearing Sciences
> > >> Boston University
> > >> 677 Beacon St.
> > >> Boston, MA 02215
> > >> Phone: (617)353-9484

Re: [Freesurfer] using custom templates

[Bruce Fischl]

yes, it does exist in that space. As long as your folding pattern atlas is 
in register with fsaverage it should work ok. But of course if your 
motivation is that your pediatric subjects have different folding patterns 
(which I'm not sure I believe unless they are *very* young), then the whole 
point is that our atlas doesn't reflect the geometry of your population

Bruce


On Thu, 5 Mar 2015, Douglas N Greve wrote:

>
> I don't think this makes sense unless you have created a new label atlas
> for your individual subjects. The current label atlas exists in the
> fsaverage space. Maybe Bruce can weigh in.
>
> On 03/05/2015 04:46 PM, Jason Tourville wrote:
>> Hi Doug,
>> Perhaps I should back up and explain our goal. We are using Freesurfer
>> to recon pediatric data sets and are planning to use the surface
>> labels as seeds for connectivity studies and for morphometric
>> analyses. We're concerned that using the fsaverage surface template as
>> the target for surface registration could introduce errors in the
>> labels due to match with our pediatric surfaces, so we derived a new
>> surface template from a subset of our data set.
>>
>> My understanding is that once we've done this, to get the surface
>> labels, stats, etc. for each scan, we need to then register each scan
>> to this new target and then run the the various steps to get the
>> labeled surfaces (e.g., mris_ca_label). So I want to confirm this;
>> more specifically, I'd like to know which steps of the recon-all
>> pipeline need to be rerun to to replace completely replace the
>> fsaverage target.
>>
>> Jason
>>
>>
>> On Thu, Mar 5, 2015 at 3:58 PM, Douglas N Greve
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> The mris_register command is what does the registration and creates a
>> new sphere.reg file. surfreg just implements that command
>> mris_register
>> command.
>>
>> I'm not sure what you mean by the labeling steps.
>>
>>
>> On 03/05/2015 03:53 PM, Jason Tourville wrote:
>>> Hi Doug,
>>> I've run the steps outlined in the SurfaceRegAndTemplates page
>> so far. So:
>>> make_average_subject --out newtemplate --subjects subj1 subj2
>> subj3 ...
>>>
>>> foreach subject (subj1 subj2 subj3 ...)
>>>cd $SUBJECTS_DIR/subject
>>>mris_register -curv surf/lh.sphere \
>>>   $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
>>>   surf/lh.sphere.reg.newtemplate
>>> end
>>>
>>> mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s
>> subj2 --s subj3 ...
>>>
>>> make_average_subject --out newnewtemplate --surf-reg
>>> sphere.reg.newtemplate \
>>>--subjects subj1 subj2 subj3 ...
>>>
>>> My understanding is that the next step is to now register each
>>> individual surface to this new template and then run through the
>>> surface (and volume) labeling steps. Is that correct?
>>>
>>> It occurs to me that the fsaverage template used as the target
>> for any
>>> .gcs that I would to label the surface. Will I have to account
>> for this?
>>>
>>> Thanks again,
>>> Jason
>>>
>>>
>>>
>>>
>>> On Thu, Mar 5, 2015 at 3:26 PM, Douglas N Greve
>>> mailto:gr...@nmr.mgh.harvard.edu>
>> > >> wrote:
>>>
>>>
>>> If you used make_average_subject to create the template, you
>> can run
>>> surfreg to do the registration. If/when you run
>> mris_preproc, make
>>> sure
>>> to spec both the target subject and the new spherical
>> registration
>>>
>>>
>>> On 03/05/2015 03:18 PM, Bruce Fischl wrote:
>>>> Hi Jason
>>>>
>>>> I don't think so - you'll probably have to edit the recon-all
>>> script. And
>>>> by template do you just mean the folding pattern .tif
>> files, or
>>> do you
>>>> meant the parcellation atlases (*.gcs)?
>>>>
>>>> cheers
>>>> Bruce
>>>> On Thu, 5 Mar 2015, Jason Tourville
>>>> wrote:
>>>>
>>>>> Greetings,
>>>>> I have generated custom surface templates from pediatric data
>>> sets. To apply
>>>>> it to the larger data set, is it sufficient to simply run the
>>> autorecon3
>>>>> steps (perhaps skipping the mris_sphere step)? If so, is
>> there
>>> a handy flag
>>>>> for running this with recon-all and/or a way to run
>> autorecon3
>>> with a flag
>>>>> indicating that the non-default template should be used?
>>>>>
>>>>> Once I've done this, I'd like to do some form of
>> comparison b/w the
>>>>> templates. I am considering looking at the overlap of surface
>>> labels
>>>>> generated by the custom templates to a manually labeled "gold
>>> standard."
>>>>> Does that sound

[Freesurfer] Cortical Misegmentation

[Pedro Rosa - Gmail]

Dear FreeSurfer, 
I have found several subjects to have temporal lobe misegmentations (usually 
neocortical, as attached, but sometimes mesial tempporal), and less frequently 
in the insula.
I could find in the manual editing page from the Wiki a way to fix this. How 
should I do it?
Thanks a lot,
Pedro Rosa.

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Re: [Freesurfer] Cortical Misegmentation

[Bruce Fischl]

What is the background image? Is it the t1 that your reconned? Can you give us 
the details about it?



> On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail  
> wrote:
> 
> Dear FreeSurfer,
> I have found several subjects to have temporal lobe misegmentations (usually 
> neocortical, as attached, but sometimes mesial tempporal), and less 
> frequently in the insula.
> I could find in the manual editing page from the Wiki a way to fix this. How 
> should I do it?
> Thanks a lot,
> Pedro Rosa.
> 
> 
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Call for participation: Fiber Tractography Challenge at ISMRM 2015

[Maxime Descoteaux]

[SORRY IF THIS IS A DUPLICATE]

Dear Colleagues: 

The Diffusion Study Group is sponsoring a novel Fiber Tractography Challenge to 
stimulate an interactive discussion on diffusion reconstruction and 
tractography methods at this year’s study group meeting at ISMRM 2015 in 
Toronto. The Challenge will use a simulated but highly realistic 
diffusion-weighted dataset in which 26 specific white matter bundles have been 
used to generate synthetic data that awaits your processing and analysis.

The Challenge, developed by diffusion experts

Peter Neher, Jean-Christophe Houde, Emmanuel Caruyer, Alessandro Daducci, Tim 
Dyrby, Klaus Maier-Hein, Bram Stieltjes, and Maxime Descoteaux

has been designed to emulate clinically-realistic acquisition. Several common 
artifacts have been introduced in the data to probe the strengths and 
limitations of your processing pipelines. All entries will receive 
individualized feedback and statistics comparing their results to the ground 
truth white matter bundles. A discussion of the methods and results will be 
held at the DSG meeting at ISMRM 2015, scheduled for Monday June 1 from 
4:30-6:30pm in Reception Hall 105.

For additional details, including information about the data, evaluation 
methods, and submission procedures, and to download the data, please visit the 
challenge website at 

http://www.tractometer.org/ismrm_2015_challenge/

An ISMRM virtual conference (date soon to be announced) will be held to present 
the Challenge, and one full hour of the study group meeting in Toronto will be 
dedicated to discussion and result presentations. Further questions regarding 
the challenge should be directed to  tractome...@gmail.com.

We look forward to seeing you in Toronto. 

Ready, track, go!

ISMRM Diffusion Study Group




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Re: [Freesurfer] read_annotation error?

[Octavian Lie]

Dear Bruce,

Reading the doc for read_annotation, it suggests that label entry
values should correspond to the colortable.table(:,5) indices. I wanted to
use it on Desikan annotation atlas and find annotation scout names for
selected cortical points:



[vertices, label, colortable] = read_annotation([some-path
'\rh.aparc.annot'], 0);

x=unique(label);
y=sort(colortable.table(:,5));

it turns out that for any of several surfaces and their corresponding rh
and lh aparc.annot I tried, x is not equal to y. Invariably,
x contains a label index 0 not present in y, and y contains indices 1639705
and 3294840 not present in x. All the other label indices match. I do not
believe destrieux annot atlas has the same problem, but I need to use
desikan's.
Please confirm this general behavior and advise.
Thank you, as always,

Octavian
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Re: [Freesurfer] Cortical Misegmentation

[Pedro Rosa - Gmail]

Hi, Bruce.
Yes, it it the T1.mgz. Is it a large topological error? Can I correct it 
editing wm.mgz?
Thanks,
Pedro.

On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote:

> What is the background image? Is it the t1 that your reconned? Can you give 
> us the details about it?
> 
> 
> 
> On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail  (mailto:pedrogomesr...@gmail.com)> wrote:
> 
> > Dear FreeSurfer, 
> > I have found several subjects to have temporal lobe misegmentations 
> > (usually neocortical, as attached, but sometimes mesial tempporal), and 
> > less frequently in the insula.
> > I could find in the manual editing page from the Wiki a way to fix this. 
> > How should I do it?
> > Thanks a lot,
> > Pedro Rosa.
> > 
> > 
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu)
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> 
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Re: [Freesurfer] Cortical Misegmentation

[Bruce Fischl]

What are your acquisition parameters, voxel size etc...?



> On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail  
> wrote:
> 
> Hi, Bruce.
> Yes, it it the T1.mgz. Is it a large topological error? Can I correct it 
> editing wm.mgz?
> Thanks,
> Pedro.
>> On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote:
>> 
>> What is the background image? Is it the t1 that your reconned? Can you give 
>> us the details about it?
>> 
>> 
>> 
>>> On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail  
>>> wrote:
>>> 
>>> Dear FreeSurfer,
>>> I have found several subjects to have temporal lobe misegmentations 
>>> (usually neocortical, as attached, but sometimes mesial tempporal), and 
>>> less frequently in the insula.
>>> I could find in the manual editing page from the Wiki a way to fix this. 
>>> How should I do it?
>>> Thanks a lot,
>>> Pedro Rosa.
>>> 
>>> 
>>> ___
>>> 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
>> 
>> 
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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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Re: [Freesurfer] Cortical Misegmentation

[Pedro Rosa - Gmail]

That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo time 
5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm.  

Pedro Rosa


On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote:

> What are your acquisition parameters, voxel size etc...?
>  
>  
>  
> On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail  (mailto:pedrogomesr...@gmail.com)> wrote:
>  
> > Hi, Bruce.
> > Yes, it it the T1.mgz. Is it a large topological error? Can I correct it 
> > editing wm.mgz?
> > Thanks,
> > Pedro.
> >  
> > On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote:
> >  
> > > What is the background image? Is it the t1 that your reconned? Can you 
> > > give us the details about it?
> > >  
> > >  
> > >  
> > > On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail  > > (mailto:pedrogomesr...@gmail.com)> wrote:
> > >  
> > > > Dear FreeSurfer,  
> > > > I have found several subjects to have temporal lobe misegmentations 
> > > > (usually neocortical, as attached, but sometimes mesial tempporal), and 
> > > > less frequently in the insula.
> > > > I could find in the manual editing page from the Wiki a way to fix 
> > > > this. How should I do it?
> > > > Thanks a lot,
> > > > Pedro Rosa.
> > > >  
> > > > 
> > > > ___
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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
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> > >  
> > >  
> >  
> >  
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Re: [Freesurfer] Cortical Misegmentation

[Bruce Fischl]

Hmmm, if you upload it we will take a look
Bruce



> On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail  
> wrote:
> 
> That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo time 
> 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm.
> 
> Pedro Rosa
> 
>> On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote:
>> 
>> What are your acquisition parameters, voxel size etc...?
>> 
>> 
>> 
>>> On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail  
>>> wrote:
>>> 
>>> Hi, Bruce.
>>> Yes, it it the T1.mgz. Is it a large topological error? Can I correct it 
>>> editing wm.mgz?
>>> Thanks,
>>> Pedro.
 On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote:
 
 What is the background image? Is it the t1 that your reconned? Can you 
 give us the details about it?
 
 
 
> On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail  
> wrote:
> 
> Dear FreeSurfer,
> I have found several subjects to have temporal lobe misegmentations 
> (usually neocortical, as attached, but sometimes mesial tempporal), and 
> less frequently in the insula.
> I could find in the manual editing page from the Wiki a way to fix this. 
> How should I do it?
> Thanks a lot,
> Pedro Rosa.
> 
> 
> ___
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 is
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 e-mail
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 HelpLine at
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Re: [Freesurfer] Cortical Misegmentation

[Pedro Rosa]

Hi,
It will upload in an hour, I guess: 
https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna?dl=0
Thanks a lot,
Pedro.

> On Mar 5, 2015, at 23:32, Bruce Fischl  wrote:
> 
> Hmmm, if you upload it we will take a look
> Bruce
> 
> 
> 
>> On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail  
>> wrote:
>> 
>> That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo 
>> time 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm.
>> 
>> Pedro Rosa
>> 
>>> On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote:
>>> 
>>> What are your acquisition parameters, voxel size etc...?
>>> 
>>> 
>>> 
 On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail  
 wrote:
 
 Hi, Bruce.
 Yes, it it the T1.mgz. Is it a large topological error? Can I correct it 
 editing wm.mgz?
 Thanks,
 Pedro.
> On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote:
> 
> What is the background image? Is it the t1 that your reconned? Can you 
> give us the details about it?
> 
> 
> 
>> On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail 
>>  wrote:
>> 
>> Dear FreeSurfer,
>> I have found several subjects to have temporal lobe misegmentations 
>> (usually neocortical, as attached, but sometimes mesial tempporal), and 
>> less frequently in the insula.
>> I could find in the manual editing page from the Wiki a way to fix this. 
>> How should I do it?
>> Thanks a lot,
>> Pedro Rosa.
>> 
>> 
>> ___
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Re: [Freesurfer] Cortical Misegmentation

[Bruce Fischl]

Can you put it on our ftp site instead?



> On Mar 5, 2015, at 9:37 PM, Pedro Rosa  wrote:
> 
> Hi,
> It will upload in an hour, I guess: 
> https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna?dl=0
> Thanks a lot,
> Pedro.
> 
>> On Mar 5, 2015, at 23:32, Bruce Fischl  wrote:
>> 
>> Hmmm, if you upload it we will take a look
>> Bruce
>> 
>> 
>> 
>>> On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail  
>>> wrote:
>>> 
>>> That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo 
>>> time 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm.
>>> 
>>> Pedro Rosa
>>> 
 On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote:
 
 What are your acquisition parameters, voxel size etc...?
 
 
 
> On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail  
> wrote:
> 
> Hi, Bruce.
> Yes, it it the T1.mgz. Is it a large topological error? Can I correct it 
> editing wm.mgz?
> Thanks,
> Pedro.
>> On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote:
>> 
>> What is the background image? Is it the t1 that your reconned? Can you 
>> give us the details about it?
>> 
>> 
>> 
>>> On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail 
>>>  wrote:
>>> 
>>> Dear FreeSurfer,
>>> I have found several subjects to have temporal lobe misegmentations 
>>> (usually neocortical, as attached, but sometimes mesial tempporal), and 
>>> less frequently in the insula.
>>> I could find in the manual editing page from the Wiki a way to fix 
>>> this. How should I do it?
>>> Thanks a lot,
>>> Pedro Rosa.
>>> 
>>> 
>>> ___
>>> 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 
>> 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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 e-mail
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 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
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 properly
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>>> 
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Re: [Freesurfer] Cortical Misegmentation

[Pedro Rosa]

Sure. How can I do it?

Sent from my iPhone

> On Mar 6, 2015, at 00:01, Bruce Fischl  wrote:
> 
> Can you put it on our ftp site instead?
> 
> 
> 
>> On Mar 5, 2015, at 9:37 PM, Pedro Rosa  wrote:
>> 
>> Hi,
>> It will upload in an hour, I guess: 
>> https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna?dl=0
>> Thanks a lot,
>> Pedro.
>> 
>>> On Mar 5, 2015, at 23:32, Bruce Fischl  wrote:
>>> 
>>> Hmmm, if you upload it we will take a look
>>> Bruce
>>> 
>>> 
>>> 
 On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail  
 wrote:
 
 That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo 
 time 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 
 256x192mm.
 
 Pedro Rosa
 
> On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote:
> 
> What are your acquisition parameters, voxel size etc...?
> 
> 
> 
>> On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail 
>>  wrote:
>> 
>> Hi, Bruce.
>> Yes, it it the T1.mgz. Is it a large topological error? Can I correct it 
>> editing wm.mgz?
>> Thanks,
>> Pedro.
>>> On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote:
>>> 
>>> What is the background image? Is it the t1 that your reconned? Can you 
>>> give us the details about it?
>>> 
>>> 
>>> 
 On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail 
  wrote:
 
 Dear FreeSurfer,
 I have found several subjects to have temporal lobe misegmentations 
 (usually neocortical, as attached, but sometimes mesial tempporal), 
 and less frequently in the insula.
 I could find in the manual editing page from the Wiki a way to fix 
 this. How should I do it?
 Thanks a lot,
 Pedro Rosa.
 
 
 ___
 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.
>> 
>> ___
>> 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
> 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 
> properly
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 ___
 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
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>>> e-mail
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>>> error
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>>> 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 

Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638

[Eiran Vadim Harel]

 Hi Doug,Thanks for your reply.This is the terminal output:
[Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% 
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm 
--nii.gz --surface fsaverage lhReading source surface 
/Applications/freesurfer/subjects/fsaverage/surf/lh.whiteNumber of vertices 
163842Number of faces    327680Total area         65416.648438AvgVtxArea       
0.399267AvgVtxDist       0.721953StdVtxDist       0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $cwd 
/Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nrcmdline
 mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm 
--nii.gz --surface fsaverage lh sysname  Darwinhostname 
Eran-Harels-MacBook-Pro.localmachine  i386user     eiranFixVertexAreaFlag = 
1UseMaskWithSmoothing     1OneSampleGroupMean 1y    
/Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gzlogyflag
 0usedti  0labelmask  
/Applications/freesurfer/subjects/fsaverage/label/lh.cortex.labelmaskinv 
0glmdir group.glmIllCondOK 0ReScaleX 1DoFFx 0wFile cesvar.nii.gzweightinv  
1weightsqrt 1Creating output directory group.glmLoading y from 
/Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gzSaving
 design matrix to group.glm/Xg.datNormalized matrix condition is 1Matrix 
condition is 1Found 149955 points in label.Pruning voxels by thr: 0.00Found 
75351 voxels in maskSaving mask to group.glm/mask.nii.gzReshaping 
mriglm->mask...search space = 36561.555889DOF = 26Starting fit and testFit 
completed in 0.0542833 minutesComputing spatial AR1 on surfaceResidual: 
ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nanWriting results  osgm    maxvox 
sig=5.1359  F=31.1425  at  index 47512 0 0    seed=1425981217mri_glmfit done
Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% 
mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166     
cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm 
--nii.gz --surface fsaverage lhSURFACE: fsaverage lhlog file is 
group.glm/cache.mri_glmfit-sim.log
cd 
/applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr/Applications/freesurfer/bin/mri_glmfit-sim--glmdir
 group.glm --cache 3 pos --cwpvalthresh .0166
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $Wed Mar  4 
20:55:33 IST 2015Darwin Eran-Harels-MacBook-Pro.local 10.8.0 Darwin Kernel 
Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 
i386eiransetenv SUBJECTS_DIR /Applications/freesurfer/subjectsFREESURFER_HOME 
/Applications/freesurfer
Original mri_glmfit command line:cmdline mri_glmfit --y ces.nii.gz --wls 
cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh
DoSim = 0UseCache = 1DoPoll = 0DoPBSubmit = 0DoBackground = 0DiagCluster = 
0gd2mtx = dodsfwhm = nanERROR: cannot find 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd
Any ideas?Thanks,Eiran
Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638
Date: Mon, 02 Mar 2015 14:17:39 -0500
From: Douglas N Greve 
Reply-To: Freesurfer support list 
To: freesurfer@nmr.mgh.harvard.edu

That is strange. Can you send the full terminal output from the first
call  to mri_glmfit-sim?
doug

On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote:
> Hello Freesurfers,
>
> I use freesurfer v5.3.0
>
> When I do group analysis correction for multiple comparisons for lh as
> follows:
>
> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir
> group.glm --nii.gz --surface fsaverage lh
>
> mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166
>
> I get this error message:
>
> ERROR: cannot find
> 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd
>
> For the mkanalysis-sess i used fwhm = 5.
>
> When i do the same for mni305 and use:
>
> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir
> group.glm --nii.gz
>
> mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166
>
> It works well without an error.
>
> Thanks,
> Eiran




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Re: [Freesurfer] Cortical Misegmentation

[Lee Tirrell]

You can find information on using our ftp site here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

Thanks,
Lee



On Mar 5, 2015, 22:16, at 22:16, Pedro Rosa  wrote:
>Sure. How can I do it?
>
>Sent from my iPhone
>
>> On Mar 6, 2015, at 00:01, Bruce Fischl 
>wrote:
>> 
>> Can you put it on our ftp site instead?
>> 
>> 
>> 
>>> On Mar 5, 2015, at 9:37 PM, Pedro Rosa 
>wrote:
>>> 
>>> Hi,
>>> It will upload in an hour, I guess:
>https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna?dl=0
>>> Thanks a lot,
>>> Pedro.
>>> 
 On Mar 5, 2015, at 23:32, Bruce Fischl 
>wrote:
 
 Hmmm, if you upload it we will take a look
 Bruce
 
 
 
> On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail
> wrote:
> 
> That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel
>size, echo time 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix
>size 256x192mm.
> 
> Pedro Rosa
> 
>> On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote:
>> 
>> What are your acquisition parameters, voxel size etc...?
>> 
>> 
>> 
>>> On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail
> wrote:
>>> 
>>> Hi, Bruce.
>>> Yes, it it the T1.mgz. Is it a large topological error? Can I
>correct it editing wm.mgz?
>>> Thanks,
>>> Pedro.
 On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote:
 
 What is the background image? Is it the t1 that your reconned?
>Can you give us the details about it?
 
 
 
> On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail
> wrote:
> 
> Dear FreeSurfer,
> I have found several subjects to have temporal lobe
>misegmentations (usually neocortical, as attached, but sometimes mesial
>tempporal), and less frequently in the insula.
> I could find in the manual editing page from the Wiki a way to
>fix this. How should I do it?
> Thanks a lot,
> Pedro Rosa.
> 
> 
> ___
> 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
 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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 http://www.partners.org/complianceline . If the e-mail was sent to
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