Hi Elizabeth, when FS computes a p-value, it computes assuming an unsigned test. When you specify a sign to mri_surfcluster (eg, --sign pos), it recomputes the p-value to take advantage of the signed test (divides the p-value by 2, same as lowing the threshold from 2 to 1.7. So try using 1.7 instead of 2 in tksurfer. Also, why are you setting a max for surfcluster? That will exclude anything above 5.
doug Elizabeth Gutierrez wrote: > Hi all, > > We're trying to create labels from a group level sig.mgh file. > However, after the labels are created and an annotation file/color > table is made, we try to view the sig.mgh file and the annotation file > in tksurfer, but they don't extactly overlap, even though they are > both configured to the same threshold (min-2 max-5). Most of the > labels are fine, but the labels closest to the the higher end of the > threshold end up being hollow, and only outline the sig.mgh clusters > instead of being completely filled out. Does that make sense? > > Here is our command for mri_surfcluster: > > mri_surfcluster --in sig.mgh --hemi lh --subject fsaverage --thmin 2 > --thmax 5 --sign pos --no-adjust --cwsig --o ./output_id --ocn > ./cluster_number --olab ./grouplabel > > Thanks in advance! > Elizabeth > > > > -- > Elizabeth C. Gutierrez > Graduate Student > Department of Brain and Cognitive Sciences > Massachusetts Institute of Technology > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list 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.
