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.

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

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