External Email - Use Caution Hi Doug, thanks for your answer!
This particular case is surface area. I thought I was using the FWHM15 smoothed data from outputted by qcache. I have no idea why FS tries to call FWHM34 in the glmfit-sim step. Should I have specified somewhere else in the commands? I will attach the log files again. Yes, I am aware I should be using permutation - I just wanted to run Monte Carlo again to compare results. Permutation was in fact how I came to use dev since mri_surfcluster did not work with my MAC. I downloaded a new patch you linked in a previous post but it produced more errors (maybe was not compiled for MAC?). Then I just tried with dev and it worked for me. But then I ran into the FWHM34 thing with Monte Carlo... Do you maybe have a mri_surfcluster available that will run permutation with MAC (High Sierra) and runs with the stable version? Thanks again, I really appreciate your help! Best, Lea __________________________________________________________________ Date: Tue, 3 Jul 2018 12:07:01 -0400 From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> Subject: Re: [Freesurfer] glmfit-sim FWHM 34? To: <freesurfer@nmr.mgh.harvard.edu> Message-ID: <d081e931-855f-f5fb-62bc-23779c295...@mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252"; format=flowed 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 Lea Backhausen, B.Sc. Wissenschaftliche Hilfskraft 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 Lea Backhausen, B.Sc. Wissenschaftliche Hilfskraft 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 Lea Backhausen, B.Sc. Wissenschaftliche Hilfskraft 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 Lea Backhausen, B.Sc. Wissenschaftliche Hilfskraft 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
cache.mri_glmfit-sim.log
Description: cache.mri_glmfit-sim.log
mri_glmfit.log
Description: mri_glmfit.log
rh.area.ADHD_COM_TD.15.mris_preproc.log
Description: rh.area.ADHD_COM_TD.15.mris_preproc.log
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