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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