External Email - Use Caution Thanks for the help!
On Wed, Dec 4, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > 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
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