How much did you smooth by? Is this thickness, area, or volume? Also, in general, you should not be using dev since it is an uncontrolled distribution (ie, there are many things in there that have not been tested). Also, I'm encouraging people to use permutation rather than monte-carlo-based correction.
On 07/03/2018 11:40 AM, Backhausen, Lea wrote: > > > 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.de_ > <https://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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
