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Dear FreeSurfer experts,
I am trying to do vertex-wise comparisons for thickness, surface area and volume between three groups with glmfit. Currently I am using the dev version (-------- freesurfer-darwin-OSX-ElCapitan-dev-20180627-4a8f901 --------) on Mac since I ran into problems with mri_surfcluster when using permutation for multiple comparison correction. That seems to work fine with the dev version.
When running Monte Carlo simulation with glmfit-sim I ran into the following error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th33/mc-z.csd
When I checked, the folder fm34 did not exist. But now I am wondering why FreeSurfer is trying to use FWHM34 from the beginning as I used FWHM15 for smoothing in the preprocession step. I see in the glmfit.log "ResidualFWHM 33.582634" - did I have to specify the smoothing kernel anywhere else ecxept from the preprocessing step?
Please find attached the log files for preprocessing, glmfit and glmfit-sim. Thank you so much for any help!
Best Lea
Lea Backhausen, B.Sc.
Student Research Assistant
Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie Tel. +49 (0)351 458-7166 Fax +49 (0)351 458-5754
Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.dehttps://deref-web-02.de/mail/client/kXc4jbFBtdU/dereferrer/?redirectUrl=http%3A%2F%2Fwww.uniklinikum-dresden.de%2F Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113