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 <mreuter@nmr.mgh.harvard.edu mailto:mreuter@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.
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