You will have to extract clusters (mri_surfcluster) to create an annotation, then use mri_segstats with the --annot option and specifying the y.mgh file as input and the output using something like --avgwf output.txt (also add --exludeid 0). The output will have a row for each frame in y.mgh (ie, each subject) and a column for each cluster
On 03/03/2016 12:43 PM, John Anderson wrote: > Hi Doug, > How can I use this statistical map ( e.g. as a mask) to calculate the > mean cortical thickness only in the areas of significant differnce > between the groups for every subject? > Bests, > John > *Sent:* Thursday, March 03, 2016 at 12:37 PM > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Qdec-statistical map > not sure what you mean. the statistical map will have a single value, > not a value for each subject > > On 03/03/2016 12:31 PM, John Anderson wrote: > > Dear FS experts, > > I am using Qdec to study the differnce in cortical thicnkess between > > two groups. > > Qdec is running a GLM analysis. This will output a statistical map > > (sig.mgh) for the differnce between the groups in cortical thicnkess. > > How can I extract the numbers of cortical thickness for every > > subject (depending on the order of subjects in Qdec table) from this > > statistical map ? > > Bests, > > John > > > > > > _______________________________________________ > > 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 > <http://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. > > > _______________________________________________ > 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
