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
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