Re: [Freesurfer] glmfit-sim FWHM 34?

[Douglas N. Greve]

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" 
> Subject: Re: [Freesurfer] glmfit-sim FWHM 34?
> To: 
> Message-ID: 
> 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 1

Re: [Freesurfer] glmfit-sim FWHM 34?

[Douglas Greve]

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 > wrote:


Also, I'm encouraging people to use permutation rather than
monte-carlo-based correction.




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Re: [Freesurfer] glmfit-sim FWHM 34?

[Ting Li]

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  wrote:
> 
> Also, I'm encouraging people to use permutation rather than 
> monte-carlo-based correction.

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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
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Re: [Freesurfer] glmfit-sim FWHM 34?

[Backhausen, Lea]

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" 
Subject: Re: [Freesurfer] glmfit-sim FWHM 34?
To: 
Message-ID: 
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 Backha

Re: [Freesurfer] glmfit-sim FWHM 34?

[Douglas N. Greve]

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_ 
> 
> 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

___
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Freesurfer@nmr.mgh.harvard.edu
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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.