That is not possible, but there is an easy work-around which is to use mri_segstats --i gamma.mgh --sum group_effectsize_clusters.txt --seg mc-z.th1.3.pos.sig.ocn.mgh --excludeid 0
On 10/09/2013 03:24 PM, Kayle Sawyer wrote: > Hi, > > Using FS 5.3, I ran a group analysis with mri_glmfit-sim to identify clusters > where my two groups differed (along with many other analyses, e.g. age slope > for each group). For each cluster, I would like to see what the mean group > difference is, in mm. So, I used this command: > > mri_segstats --i gamma.mgh --sum group_effectsize_clusters.txt --annot > fsaverage rh ./mc-z.th1.3.pos.sig.ocn.annot > > Unfortunately, mri_segstats looks in the wrong place for the annot file, > prepending "$SUBJECTS_DIR/fsaverage/label/rh." instead of looking in my > present GLM directory that I typed the command from. > > In comparison, if I manually create a label for one of the clusters from the > ocn.annot, and use the label, mri_segstats works: > > mri_segstats --i gamma.mgh --sum group_effectsize_clusters.txt --slabel > fsaverage rh ./label.th1.3.neg/rh.cluster-001.label > > This time, it doesn't try to look under fsaverage, but uses the present GLM > directory. Is there a way to override the SUBJECTS_DIR issue with --annot? I > tried without the "./", and with specifying the absolute path, but it still > pre-pended the "$SUBJECTS_DIR/fsaverage/label/rh." before the path. Or, > should I just create labels for each analysis, run mris_segstats for each > cluster, and then combine them all back together with grep? > > Thanks, > -Kayle > _______________________________________________ > 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.
