*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 <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 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 <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 <gr...@nmr.mgh.harvard.edu
>> > <mailto:gr...@nmr.mgh.harvard.edu>>:
>> >
>> >
>> > Basically looks ok. The only things that jump out at me are that
>> > you are using regheader (I would create a registration file with
>> > bbregister rather than assuming that there was no motion between
>> > the anatomical and the ASL). Where did brain.fsaverage.lh.mgh come
>> > from?
>> > doug
>> >
>> >
>> >
>> > On 2/27/15 2:16 PM, Matthieu Vanhoutte wrote:
>> >> Dear Freesurfer's experts,
>> >>
>> >> I computed some perfusion maps from ASL data. These perfusion
>> >> maps were registered on anatomical T1 and I would like to make a
>> >> group analysis on surfaces. Please find below my actual commands
>> >> in order to project these volumic maps on fsaverage then smooth
>> >> the data projected on fsaverage :
>> >>
>> >> *Project CBF maps on fsaverage* :
>> >> /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
>> >> fsaverage --interp trilin --projfrac 0.5 --hemi lh --o
>> >> lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg//
>> >> //mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
>> >> fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
>> >> rh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg/
>> >>
>> >> *Smooth the data projected on fsaverage (native ASL data size
>> >> voxel of 3mm)* :
>> >> /mris_fwhm --s fsaverage --hemi lh --smooth-only --i
>> >> lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh
>> >> --mask brain.fsaverage.lh.mgh//
>> >> //mris_fwhm --s fsaverage --hemi rh --smooth-only --i
>> >> rh.fsaverage.cbf.mgh --fwhm 3 --o rh.fwhm3.fsaverage.cbf.mgh
>> >> --mask brain.fsaverage.rh.mgh/
>> >>
>> >> Could you advise me on these two steps and tell me first if this
>> >> is the best way to project CBF maps on fsaverage, then to smooth
>> >> the data on surfaces ? Is my process could be improved ?
>> >>
>> >> Best regards,
>> >> --
>> >> -----------------------------
>> >> Matthieu Vanhoutte, MSc
>> >> Research Engineer - Department of Neuroradiology
>> >> Regional University Hospital, Lille, France
>> >>
>> >>
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>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
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