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 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!

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