Can you use mri_surfcluster to do this? It can output a binary mask, annotation, or label. You just need to give it the input and a threshold. If you just want constrain it to a given label, then you'll need to create a mask. doug
On 02/20/2015 09:14 PM, Eric Reavis wrote: > Hello Freesurfers, > > I've run into issues trying to create functionally-defined ROIs on the > cortical surface in FreeSurfer 5.3. > > I processed my functional localizer data in FsFast, which produced > nice activation maps on the cortical surface. I would like to create > ROIs from those maps (i.e., freesurfer labels) for use in other > analyses. Specifically, I'd like to select the largest significant > cluster in a particular anatomical neighborhood (lateral occipital) > and make a label with the same boundaries. > > I've used tksurfer to draw labels before (e.g., to create functionally > defined retinotopic ROIs), so I initially planned to create the ROIs > by hand in tksurfer on the inflated cortical surface. However, the > overlay threshold requires adjustment from the default value, and in > both tksurfer and tksurfer-sess I encountered the "Configure Overlay > Display" clipping error listed as a known issue in FreeSurfer 5.1 > (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes). Although the > release notes state that the error was slated to be fixed in 5.3, I > can attest that it is not, at least on my machine. I tried the .tcl > file workaround suggested for 5.1, as well as various keyboard > shortcuts to try to press the invisible 'apply' button, but to no avail. > > Since tksurfer didn't work, I next tried to use freeview to create the > labels. However, as far as I can tell, freeview doesn't yet support > drawing labels on the cortical surface, only volumetric ROIs. Is that > correct? > > I am wondering if there might be a workaround for this -- there seems > to be a functionality gap since tksurfer is no longer actively > supported but freeview is not yet fully developed. I am considering > doing this part of the processing in SUMA, since I know that the > functionality exists there, but it would be nice to be able to do > everything in freesurfer. > > Better yet, is there a freesurfer program that I could use to > automatically create labels based on the largest contiguous activation > cluster within a particular region of the parcellated brain, bypassing > the need for manual intervention? > > Thanks in advance for any suggestions, > > --Eric > > ------------------------------------------------------------------- > Eric A. Reavis, Ph.D. > Postdoctoral Scholar > Semel Institute for Neuroscience and Human Behavior > UCLA > (310) 478-3711 ext. 43382 <tel:%28310%29%20478-3711%20ext.%2043382> > > > _______________________________________________ > 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.
