surface area will be very smooth because of the jacobian correction. For that reason, you do not need to smooth very much (certainly no where near 15mm)
On 07/12/2018 04:46 AM, Backhausen, Lea wrote: > > > 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 > > > _______________________________________________ > 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.
