Dear Doug, Thank you for the answer. I will try it out.
Regards *-------------* 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 On 12 September 2017 at 01:44, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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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