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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.eduPhone 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/
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