I don't know if we are talking about the same thing.

In precedent mail you told me solution #1 was better :

*# 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*
But you told me :



*BTW, why are you changing format from w to curv? Why use curv at all? I'd
use mgz or nifti.*
At this point I don't know what this means ?

Thanks,

Matthieu

2015-03-05 17:12 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>:

>
> 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
> >     > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> >     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
> >>
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> >     --
> >     Douglas N. Greve, Ph.D.
> >     MGH-NMR Center
> >     gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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