There is not an easy way. Start by converting the annotation to a segmentation (mri_annotation2label with --seg output). Binarize the label you are interested in (mri_binarize --i annotseg.mgh --match 2021 --o rh-pericalcarine.mgh), then run mri_surfcluster --in rh-pericalcarine.mgh --thmin .5 --centroid (and other necessary args). The 2021 value is obtained from $FREESURFER_HOME/FreeSurferColorLUT.txt doug
On 03/05/2014 02:03 PM, David Phillips wrote: > Hello, > > Is there any way to extract a three dimensional coordinate representation of > the different brain regions (i.e., their centroids) that freesurfer is > estimating the cortical thickness of? > > Any help is appreciated and apologies if this question has been answered > before. > > regards, > David > _______________________________________________ > 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.
