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

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

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