Hi Rosa, the sig maps are uncorrected at the individual level. To correct them, run selxavg3-sess with the -fwhm option. This will compute the FWHM of the residuals. When that is done, look for the fwhm.dat file and get its contents.
Did you run this in the subject's native space? If so, then you will need to run a simulation. Let me know and I'll tell you how
If you can the analysis in the fsaverage space, then run
mri_surfcluster --in sig.nii.gz --thmin TT --sign abs --subject fsaverage --hemi lh --annot aparc \ --csd $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/th20/mc-z.csd \ --vwsig vwsig.nii.gz --cwsig cwsig.nii.gz --fwhm fwhm.dat --mask mask.nii.gz --sum sum.dat
Where TT is the voxel-wise threshold (cluster forming threshold), --sign abs means take positive or negative, XX is the FWHM (rounded up to next integer). The output vwsig is the volume corrected for voxel-wise significance, cwsig is the clusteriwise significance.
doug
On 3/12/13 8:35 PM, Rosa Lafer-Sousa wrote:
Hi Doug, I am analyzing data for two monkeys and I am under the impression that I should be correcting each independently for every contrast I generate. I also run stxgrinder-sess after I run mkcontrast to generate the contrasts. Are the significance maps yielded by these two steps constructed from uncorrected p-values? I want to make sure I correct for multiple comparisons within each voxel, and I assumed this was being taken care of internally by these steps... if it is not, how would you suggest I go about doing so?
thanks, Rosa
On Tue, Mar 12, 2013 at 3:26 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Rosa, it does not. Usually correction is done at the group level. Do you need to do it on an individual? doug On 3/12/13 6:27 PM, Rosa Lafer-Sousa wrote:Hi freesurfers! I am curious about corrections for multiple comparisons. I use mkcontrast to generate my statistical maps and am curious if the function provides any internal corrections for multiple comparisons Does mkcontrast-sess correct for multiple comparisons? If so, how? thank you, Rosa -- Rosa Lafer-Sousa Lab Manager, Conway Lab Wellesley College - Neuroscience 106 Central Street Wellesley, MA Harvard Medical School -Neurobiology 220 Longwood Ave WAB Rm 215 Boston, MA 02115 210-325-3185 rlaferso@wellesley.edu <mailto:rlaferso@wellesley.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.-- Rosa Lafer-Sousa Lab Manager, Conway Lab Wellesley College - Neuroscience 106 Central Street Wellesley, MA
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