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 <gr...@nmr.mgh.harvard.edu 
> <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
>     <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>     > <mailto: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>>
>     >     > <mailto: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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>     MGH-NMR Center
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