External Email - Use Caution
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
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
External Email - Use Caution
Hi Douglas,
I try to use permutation but it takes forever. I never see the end. Do I have to update the freesurfer to use the permutation? As it was recommended in this year?
Best, Ting
On Jul 3, 2018, at 11:07 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Also, I'm encouraging people to use permutation rather than monte-carlo-based correction.
can you send more info? command line, terminal output, what you are analuyzing, etc. If the fwhm is still 34, then something may be wrong.
On 7/12/18 11:48 AM, Ting Li wrote:
External Email - Use Caution
Hi Douglas,
I try to use permutation but it takes forever. I never see the end. Do I have to update the freesurfer to use the permutation? As it was recommended in this year?
Best, Ting
On Jul 3, 2018, at 11:07 AM, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Also, I'm encouraging people to use permutation rather than monte-carlo-based correction.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Backhausen, Lea -
Douglas Greve -
Douglas N. Greve
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Ting Li