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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" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] glmfit-sim FWHM 34? To: freesurfer@nmr.mgh.harvard.edu Message-ID: d081e931-855f-f5fb-62bc-23779c295624@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.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
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.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
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.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
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.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
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" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] glmfit-sim FWHM 34? To: freesurfer@nmr.mgh.harvard.edu Message-ID: d081e931-855f-f5fb-62bc-23779c295624@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
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Douglas N. Greve