Is the mc-zabs annot based on thickness differences? If so, you can run mri_segstats on the stack from each time point, eg,
mri_segstats ---annot fsaverage lh /path/to/mc-zabs.the13sig.ocn.annot --i timepoint1.lh.stack.mgh --avgwf timepoint1.lh.stack.dat --excludeid 0 this will create the .dat file with a row for each input in the stack and a column for each cluster On 05/16/2016 09:43 AM, Liu Y wrote: > Dear Martin and Douglas, > > I created the cluster ROIs (mc-zabs.the13sig.ocn.annot) for the two > groups. What is the detailed command line to calculate the baseline > and followup cortical thicknesses from the *.long.* directories? > > Thanks, > Yawu > > On Thu, May 12, 2016 at 9:07 PM, Martin Reuter > <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> wrote: > > Hi Yawu, > > and both baseline and follow-up surfaces (from the *.long.* > directories) > are in vertex correspondence, so you can use the ROI on each time > point > directly. > > Best, Martin > > On 05/12/2016 02:00 PM, Douglas N Greve wrote: > > If you used mri_glmfit, then you can use mri_glmfit-sim to create > > significant clusters. It will create an annotation of the > significant > > clusters, and you can pass that to mri_segstats along with the > stack of > > thickness images to extract the mean thickness in each cluster. > > > > On 05/12/2016 04:23 AM, Liu Y wrote: > >> Hi Freesurfers, > >> > >> I am using the degree of cortical atrophy between two groups. The > >> atrophy rate had no significant difference between two groups, > but the > >> average thickness of the baseline and followup showed significant > >> clusters in two regions between the two groups. My question is > how to > >> create the ROIs covering the clusters, and then extract the > >> thicknesses on baseline and followup MRIs? > >> > >> Thanks, > >> Yawu > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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
