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_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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of mariangela asimina
<mariang...@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
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