Dear Doug, After some trial and error I am still not able to run group analysis in ROI manner.
Here is my understanding: I need to define a label (mri_binarize ?) in which my ROIs should be labeled as 1 with other regions being 0. Then I can take this label to glm with --lable and then run correction. If this is a right way can you tell me a little bit more of how to do this. I am working on cortical thickness data. Thanks huge *-------------* 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 08:42, Xianwei Che <xianwei....@monash.edu> wrote: > 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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