Yes, but threshold it first, eg mri_binarize --abs --i sig.cluster.mgh --min .000001 --o newmask.mgh
On 12/4/19 1:38 PM, cody samth wrote: > > External Email - Use Caution > > Thanks, for your input. It's interesting that there isn't a more > standard way of approaching it. If i wanted to constrain my post-hoc > to be within the cluster(s) from the main effect how would I go about > running this through mri_glmfit? Would I include the --mask > sig.cluster.mgh in the command for mri_glmfit and then aslo > mri_glmfit-sim? > > On Mon, Dec 2, 2019 at 6:40 PM Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > I don't think there is a standard way to do this. A vertex-wise > analysis is not the same thing as a averaging over a group of > vertices. I guess you could constrain your post-hoc analysis to be > within the main effect cluster; that would be most consistent. But > I don't think you'd have any problems getting it published either way. > > On 12/2/2019 3:12 PM, cody samth wrote: >> >> External Email - Use Caution >> >> Hi, >> >> I have a statistical question about how to approach reporting >> results from FreeSurfer analyses containing three groups. I ran a >> group effect (F-test) and then post-hoc tests looking at >> pair-wise comparisons between the three groups. My question is >> why is that we run separate vertex-wise analyses for the >> post-hocs rather than extracting the values from significant >> clusters and running post-hocs in a statistical software for just >> the regions where a significance difference was found (ie the >> clusters)? As a post-hoc vertex wide analysis can lead to >> different results. >> >> For example in my group effect contrasts I found a cluster in the >> parietal lobe. Whereas in my post hoc-vertex wide analyses one of >> them found two clusters 1) within the parietal 2) within the >> frontal lobe. If I choose to run these post-hoc analyses via >> freesurfer (ie vertex-wise) rather than extracting the results to >> analyze in a statistical program, is it standard to report the >> second cluster? Even though it didn't come up in the group model? >> If so is there a paper that people reference that uses this approach? >> >> Thanks, >> Cody >> >> _______________________________________________ >> 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
