Dear Freesurfer experts, I have been using Freesurfer in combination with rtview.sh to visualize my retinotopic mapping results (rotating wedge) and to define masks for individual visual areas. The command that I use for this is something like:
rtview.sh --s *subj_id* --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz --fsig polar/fsig.nii.gz I was under the impression that by specifying fsig, Freesurfer would internally threshold the resulting polar map according to an F-test to show only significant vertices. Is this true? I actually doubt that this is the case because I noticed in the "configure overlay display" that the maps are seemingly arbitrarily thresholded at a "Min" of 0.4. Is this threshold derived based on statistical principle? How can I do proper statistics with fsig.nii.gz in Freesurfer, i.e. define alpha, correct for multiple comparisons etc.? Thanks, Michael P.S.: Just to provide some context for my question... imho it doesn't matter much if a given vertex is significantly activated if the only purpose is to define boundaries between visual areas. However, an exception would be the definition of such boundaries in the cortical surface near the fovea where boundaries between areas cannot be identified as reliably as in more eccentric regions. I was thinking that by focusing only on significant vertices, I would be able to isolate only those voxels that can clearly be assigned to a single visual area - even if that means that I may have to discard some vertices near the fovea. -- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031
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