Hi Stefano,
Here's what you can do. In your shell (assuming you are using c shell)
# First set variable s to be subject id
set s = 100306_QD95CU_FS
# set freesurfer environmental variable SUBJECTS_DIR to point to where the data is
setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
# use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
# use "-sval-annot" option to transfer annotation
mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval-annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
# use "sval" option to transfer confidence map.
mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
Cheers, Thomas
On Sun, Jul 20, 2014 at 10:33 PM, stdp82@virgilio.it wrote:
Hi list and Thomas,
I'm running the first step to use Yeo's parcellation. The running is wrong.
mri_surf2surf --s Control01 --hemi lh --sval-tal-xyz white --tval lh.white.Control01 --tval-xyz --trgsubject fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz
Reading target surface reg $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg MRISread( $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg): could not open file Not a directory mri_surf2surf: could not read surface $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg
Thanks,
Stefano
----Messaggio originale---- Da: ythomas@csail.mit.edu Data: 7-feb-2014 9.49 A: stdp82@virgilio.it Cc: "freesurfer"freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Yeo parcellation
Hi Stefano,
A) From FreeSurfer 5.2 onwards, the Yeo parcellation files can be found inside $FREESURFER_HOME/subjects/fsaverage/label/, so you can simply use those files there instead of downloading from the wiki.
B) You can use mri_surf2surf to transform the annot files from the fsaverage "subject" to the individual subjects' surface. There is an example of how to do it if you run "mri_surf2surf --help"
C) Once you have created the subject's specific annot file from part B, I believe you must first run mris_anatomical_stats, and then run aparcstats2table. However, I am not sure about this, so someone on the list should correct me if I am wrong!
Regards, Thomas
On Fri, Feb 7, 2014 at 3:58 PM, stdp82@virgilio.it wrote:
Hi list,
I have download the files of Yeo parcellation from ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip.
I have two questions, please.
A- Which is the directory where I should put these files? B-I have already run by recon-all -all all my subjects. How can I added to them Yeo parcellation? C-I'd like also calculate the cortical thickness for each Yeo's ROI. Is possible with aparcstats2table?
Thanks.
Regards,
Stefano
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