Dear Doug, thank you so much for the feedback and all of your help!
Best wishes Marco On Thu, Jul 6, 2017 at 1:45 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > You can use mri_surfcluster. Set the sig.mgh as the --in file. Set --fdr > to the FDR you want. Set --subject fsaverage and set the ---hemi. Set > --annot aparc. Set --sum to the output summary file. This should give you > something similar to the output of mri_glmfit-sim. > > On 6/29/17 4:29 PM, marco mcsweeney wrote: > > Dear FreeSurfer experts, > > I ran my group analysis using mri_glmfit and found a number of significant > clusters showing cortical thickness differences between 2 groups. I used > tksurfer to visualize the results and used FDR to correct for multiple > comparisons. > > My question is about how do I correctly get the FDR corrected results > showing cluster number, size, MNI coordinates etc. as I would if I used > QDEC? > > I have searched through the archives and have found what looks like the > answer, but I'm not convinced that the method I used is correct. > > I used > > 1) mri_glmfit-sim --glmdir lh.group_diff.glmdir --cache 1.3 abs > --cwpvalthresh .99 > > and > > 2) less lh.group_diff.glmdir/contrast.txt/cache.th13.abs.sig. > cluster.summary > > However when I visualize the FDR corrected results with tksurfer or > freeview I can see a couple of clusters not listed in the summary. Am I > missing something? > > Thank you so much in advance. > > Any help or advice would be greatly appreciated. > > Best wishes > > Marco > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > 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. > >
_______________________________________________ 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.
