External Email - Use Caution
Hello FreeSurfer developers and experts,
I am trying to do cluster correction with mri_glmfit-sim after running mri_glmfit.
The command I ran: mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs --cwp 0.05 --2spaces
produces the following error: ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Operating System: Ubuntu 22.04.2 LTS Kernel: Linux 5.19.0-35-generic
I have searched the archive and cannot find a similar error. I would appreciate your help.
Mariangela Asimina
I also ran the command with the --debug flag and I get the following output, but I'm afraid I can't interpret it: set echo = 1 ; breaksw breaksw
end end while ( $#argv != 0 ) while ( 8 != 0 )
set flag = $argv[1] ; shift ; set flag = --glmdir shift
switch ( $flag ) switch ( --glmdir ) if ( $#argv < 0 ) goto arg1err ; if ( 7 < 0 ) goto arg1err set glmdir = $argv[1] ; shift ; set glmdir = lh.volume.SCNStudyTest.10.glmdir shift breaksw breaksw
end end while ( $#argv != 0 ) while ( 6 != 0 )
set flag = $argv[1] ; shift ; set flag = --cache shift
switch ( $flag ) switch ( --cache ) if ( $#argv < 2 ) goto arg2err ; if ( 5 < 2 ) goto arg2err set thresh = $argv[1] ; shift ; set thresh = 3.0 shift set simsign = $argv[1] ; shift ; set simsign = abs shift set UseCache = 1 ; set UseCache = 1 set DoSim = 0 ; set DoSim = 0
set thresh = `echo $thresh | sed 's/,/./g'` set thresh = `echo $thresh | sed 's/,/./g'` sed s/,/./g echo 3.0 set thresh = `printf %2.1f $thresh` set thresh = `printf %2.1f $thresh` printf %2.1f 3.0 if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 3.3 && 3,0 != 4.0 ) then echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0" echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 exit 1 ; exit 1
External Email - Use Caution
I see now this is an issue addressed stable 7.2.0 version of FreeSurfer: https://secure-web.cisco.com/1_0nM8kQPAwlCZzUFPKYxFeyxAfrBfjVnMbuFBgpiLtOtAz...
mri_glmfit-sim
* Fixed locale issue to handle cases where decimal points are represented by commas.
Is it ok to install the newest version (7.3.2) and run mri_glmfit-sim on data made with the version I used? Is it ok to troubleshoot the recon-all output that I already have, after installing the newer version? Or would I have to run the recon-all again?
Lastly, if the answer to the above is negative, is it possible to solve the issue with the commas on the version I am using?
Thank you! Mariangela
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of mariangela asimina mariang_as@hotmail.com Sent: Monday, March 20, 2023 8:13 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_glmfit-sim error
External Email - Use Caution
Hello FreeSurfer developers and experts,
I am trying to do cluster correction with mri_glmfit-sim after running mri_glmfit.
The command I ran: mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs --cwp 0.05 --2spaces
produces the following error: ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Operating System: Ubuntu 22.04.2 LTS Kernel: Linux 5.19.0-35-generic
I have searched the archive and cannot find a similar error. I would appreciate your help.
Mariangela Asimina
I also ran the command with the --debug flag and I get the following output, but I'm afraid I can't interpret it: set echo = 1 ; breaksw breaksw
end end while ( $#argv != 0 ) while ( 8 != 0 )
set flag = $argv[1] ; shift ; set flag = --glmdir shift
switch ( $flag ) switch ( --glmdir ) if ( $#argv < 0 ) goto arg1err ; if ( 7 < 0 ) goto arg1err set glmdir = $argv[1] ; shift ; set glmdir = lh.volume.SCNStudyTest.10.glmdir shift breaksw breaksw
end end while ( $#argv != 0 ) while ( 6 != 0 )
set flag = $argv[1] ; shift ; set flag = --cache shift
switch ( $flag ) switch ( --cache ) if ( $#argv < 2 ) goto arg2err ; if ( 5 < 2 ) goto arg2err set thresh = $argv[1] ; shift ; set thresh = 3.0 shift set simsign = $argv[1] ; shift ; set simsign = abs shift set UseCache = 1 ; set UseCache = 1 set DoSim = 0 ; set DoSim = 0
set thresh = `echo $thresh | sed 's/,/./g'` set thresh = `echo $thresh | sed 's/,/./g'` sed s/,/./g echo 3.0 set thresh = `printf %2.1f $thresh` set thresh = `printf %2.1f $thresh` printf %2.1f 3.0 if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 3.3 && 3,0 != 4.0 ) then echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0" echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 exit 1 ; exit 1
Yes, all the 7.X versions will give the same answer unless you explicitly use a new feature
On 3/20/2023 2:45 PM, mariangela asimina wrote:
External Email - Use Caution
I see now this is an issue addressed stable 7.2.0 version of FreeSurfer: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes https://secure-web.cisco.com/1_0nM8kQPAwlCZzUFPKYxFeyxAfrBfjVnMbuFBgpiLtOtAz0Rcg2ns0AHK0Z-UuAC0K-jylD0ZM1hP4emJWrKoCvyUwJv4VVaznUFGMKUwg5OuApejYTaxHdKuzNe5HOOGskw2aVkgC0HOeyCPniLzoA5MSfRjpv1RfRJdNli3dKvwIjsY48WuxJT69HBkSXeu374bWB2rlhnP3OpNcmqdmIzR2dm46aiVRBcm3JvbkQLgtvhZeadmj2hfxQUQPDJYVfkQcP70pazbHOft-_rcNzvPKYmvvAAelzNeTuwNBoa1gQT-rqipRmHUXA8AhgFoON7c7sEJ06rpAXxn2QgBw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
mri_glmfit-sim
- Fixed locale issue to handle cases where decimal points are represented by commas.
Is it ok to install the newest version (7.3.2) and run mri_glmfit-sim on data made with the version I used? Is it ok to troubleshoot the recon-all output that I already have, after installing the newer version? Or would I have to run the recon-all again?
Lastly, if the answer to the above is negative, is it possible to solve the issue with the commas on the version I am using?
Thank you! Mariangela
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of mariangela asimina mariang_as@hotmail.com *Sent:* Monday, March 20, 2023 8:13 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] mri_glmfit-sim error
External Email - Use Caution
Hello FreeSurfer developers and experts,
I am trying to do cluster correction with mri_glmfit-sim after running mri_glmfit.
The command I ran: mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs --cwp 0.05 --2spaces
produces the following error: ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Operating System: Ubuntu 22.04.2 LTS Kernel: Linux 5.19.0-35-generic
I have searched the archive and cannot find a similar error. I would appreciate your help.
Mariangela Asimina
I also ran the command with the --debug flag and I get the following output, but I'm afraid I can't interpret it: set echo = 1 ; breaksw breaksw
end end while ( $#argv != 0 ) while ( 8 != 0 )
set flag = $argv[1] ; shift ; set flag = --glmdir shift
switch ( $flag ) switch ( --glmdir ) if ( $#argv < 0 ) goto arg1err ; if ( 7 < 0 ) goto arg1err set glmdir = $argv[1] ; shift ; set glmdir = lh.volume.SCNStudyTest.10.glmdir shift breaksw breaksw
end end while ( $#argv != 0 ) while ( 6 != 0 )
set flag = $argv[1] ; shift ; set flag = --cache shift
switch ( $flag ) switch ( --cache ) if ( $#argv < 2 ) goto arg2err ; if ( 5 < 2 ) goto arg2err set thresh = $argv[1] ; shift ; set thresh = 3.0 shift set simsign = $argv[1] ; shift ; set simsign = abs shift set UseCache = 1 ; set UseCache = 1 set DoSim = 0 ; set DoSim = 0
set thresh = `echo $thresh | sed 's/,/./g'` set thresh = `echo $thresh | sed 's/,/./g'` sed s/,/./g echo 3.0 set thresh = `printf %2.1f $thresh` set thresh = `printf %2.1f $thresh` printf %2.1f 3.0 if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 3.3 && 3,0 != 4.0 ) then echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0" echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 exit 1 ; exit 1
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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Douglas N. Greve -
mariangela asimina