On 09/10/2017 04:02 AM, Xianwei Che wrote: > Dear experts, > > I am going to run a group analysis on thickness but limit the results > to certain regions, say prefrontal cortex. l did find this thread but > failed to make it work on my data > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html). > I know I could extract the signal of the ROI but also interested in > this way. > > Here are my questions: > 1. mri_binarize should be working on the average data or the single > data in each participant. If it should be on individual data, what the > loop should be (if I have a text file SUBJECTS listing the participants). Actually, I don't know what [subjects] is supposed to mean. You should include the index for the ROIs you want in the analysis > 2. How the --match is used. I --helped the mri_binarize but did not > get it. Is it for specifying the ROI by number, say the number of PFC? There is no PFC ROI. You will have to piece it together from other ROIs. You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt. Look in the section for aparc+aseg.mgz > 3. If I could finish the mask creation and merge to label; do I have > to undergo the data concatenating stage (i.e. preproc, surf2surf) or > directly move to glm. I saw another thread skipping these stages but > it's on volume data > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html). Yu can move directly to the GLM > > Thank you so much! > > > /-------------/ > Mr Xianwei Che > PhD Candidate > Monash Alfred Psychiatry Research Centre (MAPrc) > Central Clinical School & the Alfred > Monash University > Level 4, 607 St Kilda Road, Melbourne 3004, Australia > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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