On Oct 12, 2016, at 11:59 PM, tom parker <tomparker540@gmail.com> 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!

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer