#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
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