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>: > 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>: > >> 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 >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >
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