External Email - Use Caution

Hello experts,

I am going through FreeSurfer's repeated measures anova tutorial using fspalm. I understand that fspalm frontend can only do t-tests at the moment and NOT F tests as noted in this thread: https://secure-web.cisco.com/1t11cJOK6FCdHxqm_O6WFHk15uAjWyctjoR7VAvgTW5hEaA...

So I am trying to run F-contrast on PALM but I was wondering if I also have to worry about bonferroni clusterwise correction. If I used --2spaces option when using fspalm frontend, I thought I should also try to apply the equivalent bonferroni correction when running F-test on FSL palm.

For the F-test on FSL palm, it looked like I could run the following command with the addition of -f and -ftestonly flags (shown in underline):

palm -i lh.thickness.mgz -i rh.thickness.mgz -d design.mat -t design.con *-f design.fts* -o myresults -n 2000 -corrcon -corrmod *-ftestonly*

taken from this email thread- https://secure-web.cisco.com/1vFEFTKkUMsHsCHW3u3SsOIpxhqtkKCXdjWw6TLTufeciiV...

Would this be equivalent to the bonferroni correction methods that fspalm uses? When I go through fspalm.log it seemed to run mri_surfcluster and mri_segstats after running fspalm with certain commands having --sig2p-max and --bonferroni-max 2 flags.

Thank you in advance for your help!

Best, Julia Shin