usually the fsaverage mask is fine. You can use mri_label2label with the --outmask option to convert the ?h.cortex.label to a binary mask. You can also pass surfcluster a label directly with the --clabel option
On 05/14/2017 05:45 AM, Ryan Muetzel wrote: > Dear Experts, > > This is partially a follow-up question to another thread related to > the mask.mgh generated by mri_glmfit > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50691.html). > > We would like to use the mri_surfcluster tool on a log10p map. I’m > wondering — for vertex-wise analyses that use freesurfer-specific > output (e.g., thickness, surface area, lgi, etc, not FMRI or DTI > data)….can we rely on a single mask image for each hemisphere that > comes from the fsaverage ?h.cortex.label? Or, should we be creating a > mask that is specific to a given analysis/dataset, as is done with > mri_glmfit? > > If the latter, is there a way to create this mask outside of mri_glmfit? > > Thank you in advance for your time and help! > > Best, > > Ryan > > > > _______________________________________________ > 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.
