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_O6WFHk15uAjWyctjoR7VAvgTW5hEaA9_sjyiYALB2fXd9m-FBh0Kg1PL3ad0gmauXJptgr0OsSWIvH5yvW90C6JcTsY4dGgSxgdJoupwln1lD4NF5DCNyY4MC94KrGS6gjEl1Ef6mnRQ8DaPW6IPC52_OSOeQ6yIFJk-pIQ_l6hU36sO0w4ltduXeRUdUWUoi76970J03S0tfYdkXYyb2NdDj1k0tZcwBlo0R-ZbSHw2T1PE1g-d7qZ_Z44hYS4u0cjJ0E-lojR-V2PxgCrMFthMVIPZorvaHSNYacIejldVs_yR/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg68722.html 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/1vFEFTKkUMsHsCHW3u3SsOIpxhqtkKCXdjWw6TLTufeciiVfUYjAr_XeZnYwIKAUVRX_dO9rzxwwyR9rR6mSBffHF-vk47xcYk6DDpo0bN5Vg914LJHctM8q7zowkBB5l_I6yZHOhfRsx6n8JTmTmVY6Bms3mgy1N20o6t8pg_u1hnZFtegys2UKbC4eNBHhiJL4vwbbgRN9qWob_BqGSuLcDDqWMNWy_eej8I91a1cHluQ1WnvPWNeXmN77iNJuL97H0qkQ36AGdFY35H0dzit5mMc1n5U1rdNXpLXRkzdg8TUHW0lLth6szSrfwbb4N/https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FA2%3DFSL%3B42baf4dd.1608 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
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