You'll need to get a copy of mri_surf2surf.{linux,mac}. It was there all
the time I just did not put it on the installation page. I've updated
the page with this link
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mri_surf2surf.{linux,mac}
When you re-run delete the xhemi folder if it exists.
On 01/23/2015 12:32 PM, Alexandre Routier wrote:
> Hello everyone,
>
> I have a new question concerning fsaverage: I would like to perform
> some asymmetry analyses but I noticed that the left and right
> hemispheres were not symmetric.
>
> I found here ( https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi ) how
> to register a subject to fsaverage_sym but I have some issues.
> "surfreg --s $subject --t fsaverage_sym --lh" worked fine (see first
> log file) and the ${subject}/xhemi/surf/ folder is empty.
> Then "surfreg --s $subject --t fsaverage_sym --lh --xhemi" (see second
> log file) didn't work because ${subject}/xhemi/surf/lh.sphere was not
> found. Did I miss something ? I modified FS 5.1 thanks to the section
> "Installation" concerning my configuration.
>
> Moreover, I cannot test yet but I would like to know if the following
> commands will work for a single subject:
> mris_preproc --target fsaverage_sym --hemi lh \
> --xhemi --paired-diff \
> --srcsurfreg fsaverage_sym.sphere.reg \
> --meas thickness \
> --out lh.lh-rh.thickness.sm00.mgh \
> --s ${name_subject}
>
> # Smooth e.g. 10mm of the surface
> mris_fwhm --s ${name_subject} --hemi lh --cortex --smooth-only --fwhm
> 10 --i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm10.mgh
>
> # Analyze
> mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
> glm.lh.lh-rh.thickness.sm10 --osgm --surf ${name_subject} lh
>
> I slightly modified the commands on the tutorial for my needs but I
> can't check for the moment.
>
> Thanks in advance for your help.
>
> Best regards,
> Alexandre
>
>
> 2014-12-05 12:09 GMT+01:00 Alexandre Routier
> <alexandre.rout...@gmail.com <mailto:alexandre.rout...@gmail.com>>:
>
> Hello,
>
> Thanks for your answers :)
>
> mri_annotation2label enabled me to convert the ROI of Desikan
> Atlas as I wanted and the Brodmann were indeed in
> $FREESURFER_HOME/subjects/fsaverage/label .
>
> Have a nice day,
> Alexandre
>
>
> 2014-12-04 23:01 GMT+01:00 Bruce Fischl
> <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>:
>
> Hi Alexandre
>
> I'm not entirely sure what you are asking, but the fsaverage
> Brodmann areas and parcellations should all be stored in the
> directory:
>
> $FREESURFER_HOME/subjects/fsaverage/label
>
> cheers
> Bruce
>
>
>
> On Thu, 4 Dec 2014, Alexandre Routier wrote:
>
> Hello,
>
> I am currently working with cortical thickness and more
> particularly with
> the fsaverage. Since the thickness has the same number of
> voxel, I would
> like to correspond the voxels with some ROI, for instance the
> Desikan-Killiany Atlas or the Brodmann area.
>
> Are they any label or text files which correspond a ROI
> with the indices of
> the voxels in fsaverage ?
>
> Thanks in advance for you help,
> Alexandre
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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