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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