Pass it with --mask, not --label
On 09/11/2017 09:42 PM, Xianwei Che wrote: > 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 > <mailto: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 <mailto: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 > > <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 > > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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. > > > > > > _______________________________________________ > 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
