How did you create the ROIs? On 07/01/2015 12:25 PM, Martin Hebart wrote: > Dear members of the list, > > I'm new to Freesurfer, so please excuse me asking possibly basic > questions. I have spent quite some time on the wiki and searching > through the emails before writing to the list, but I might have missed > some important information. > > I would like to work on anatomical ROIs created based on Freesurfer's > surface-based and volumetric ROIs and continue working with them in > nifti format (e.g. for SPM). If I understand it correctly, the > surface-based ROIs should take into account the individual subject's > anatomy better than the volumetric ROIs would. At the same time, for > subcortical regions it is necessary to use volumetric ROIs. > > I did recon -all, followed by extracting all surface ROIs using > mri_label2vol --annot aparc.a2009s.annot and the volumetric ROIs using > mri_label2vol --seg aparc.a2009s+aseg.mgz . Finally, I manually > removed all cortical labels from the volumetric ROIs. > > Now when looking at the ROIs, they overlap slightly, both between left > and right hemisphere (roughly 150 voxels), and between the hemispheres > and the subcortical regions (roughly 300 voxels). > > Is there a way I can assign the masks volumes a unique label? I was > considering removing these voxels, but ideally I would just keep them > in and use the label with the highest probability. Or is there an > alternative suggestion that makes more sense (e.g. rather attributing > overlapping regions to subcortical regions)? > > Thanks a lot in advance for your reply! > Martin > > > _______________________________________________ > 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.
