Hi Doug,
Thanks for your help. I think the most important thing for me was to know that the vertices are thresholded by default at p < .01. So that is good news! I was just a little worried that the thresholding I see was arbitrary and might even be inconsistent across subjects.
In that case I don't think I will have to do my own thresholding or correction for multiple comparisons.
Just out of curiosity: If I wanted to threshold at, say, p < .05, how would I implement that using rtview?
Best, Michael
On Jul 15, 2013, at 8:48 PM, Douglas N Greve wrote:
This interface is a little complicated and not intuitive. The map you see is an angle map thresholded at p<.01. This thresholding is done internally and has nothing to do with the Min/Max/Slope.
If you want to correct for multiple comparisons, then you will need to run selxavg3-sess with -fwhm (a hidden option) to compute the FWHM.
You will then need to run a simulation to get correction tables. You can do this with mri_mcsim, something like
mri_mcsim --o youroutputfolder --base mc-z --fwhm-max yourfwhmrounded --mask mask.nii.gz --surface yoursubject lh --nreps 10000
where youroutputfolder is just a place to put the output yourfwhmrounded is the FWHM computed by selxavg3-sess above rounded to the next higher integer mask.nii.gz is the mask from the selxavg3-sess analysis
Once that done (may take a few hours or longer), you can then run mri_surfcluster to do the actual correction. Let me know if you need help once you get there
doug
On 07/15/2013 12:31 PM, Michael Bannert wrote:
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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-- 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