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 <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 <gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> >
> > On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> > > Dear Doug,
> > >
> > > Thank you for helping !
> > >
> > > Yes I directly used the regheader option because in the steps
> > before I
> > > already registered ASL maps on anatomical 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>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>>:
> > >
> > >
> > > Basically looks ok. The only things that jump out at me are
> that
> > > you are using regheader (I would create a registration file
> with
> > > bbregister rather than assuming that there was no motion
> between
> > > the anatomical and the ASL). Where did
> > brain.fsaverage.lh.mgh come
> > > from?
> > > doug
> > >
> > >
> > >
> > > 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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