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Hi FreeSurfer community,

I’m using fspalm to correct multiple comparisons for vertex-based cortical thickness analysis. It ran successfully and several clusters survived after correction for multiple comparisons. Below is the code I used for permutation tests.

fspalm --glmdir cth.glmdir --cft 4 --onetail --name palm-onetail-4 --iters 1000 --2spaces --cwp .05

After that, I would like to generate a surface map after permutation tests, which stores the original surface values except that vertices not assigned to a cluster are set to 0. I checked the fspalm and mri_surfcluster description but did not find any clue.

I also tried to run the analysis below but I could not adjust the threshold of the output file (contrast.surfvalues.mgz) because it seems to be a binary file .

mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030 --subject fsaverage --hemi lh --annot aparc --no-fixmni --surf white --ocn contrast.ocn.mgz --oannot ./contrast.ocn.annot --sig2p-max --bonferroni-max 2 --o ./contrast.surfvalues.mgz

Any help would be appreciated. 

Thanks,
Isabelle