Hi Tom,
Could be the qdec table has weird characters.
Try with a simplified table (only a few rows, created in a text editor from
scratch, space separated).
best, Martin
> On Oct 12, 2016, at 11:59 PM, tom parker wrote:
>
> Dear FreeSurfers,
>
> I've been trying to run a longitudinal cortical thickness analysis in
> FreeSurfer but unfortunately, so far, it has not worked.
>
> After preprocessing the data following the instructions from the tutorial, I
> tried running:
> long_mris_slopes --qdec /Volumes/WD/Long/qdec/long.qdec.table.dat --meas
> thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack
> --do-label --time years --qcache fsaverage --sd /Volumes/WD/Long/
>
> And the following error came out:
> Parsing the qdec table: /Volumes/WD/Long/qdec/long.qdec.table.dat
> ERROR: qdec table /Volumes/WD/Long/qdec/long.qdec.table.dat not found or
> empty?
>
> The path is correct and there are no empty lines in the file.
>
> When I ran:
> mris_preproc --debug --qdec-long qdec/long.qdec.table.dat
>
> This comes out:
> set echo = 1 ;
> set debug = 1 ;
> set debug = 1
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 2 != 0 )
>
> set flag = $argv[1] ; shift ;
> set flag = --qdec-long
> shift
>
> switch ( $flag )
> switch ( --qdec-long )
> if ( $#argv == 0 ) goto arg1err ;
> if ( 1 == 0 ) goto arg1err
> set fsgdf = $argv[1] ; shift ;
> set fsgdf = qdec/long.qdec.table.dat
> shift
> if ( ! -e $fsgdf ) then
> if ( ! -e qdec/long.qdec.table.dat ) then
> echo "ERROR: cannot find $fsgdf" ;
> echo ERROR: cannot find qdec/long.qdec.table.dat
> ERROR: cannot find qdec/long.qdec.table.dat
> exit 1 ;
> exit 1
>
> Do you have any idea why this is happening?
>
> Thank you so much!
>
>
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