On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:

Hi Chris,

this is a good question for the list (cc'ed), others may or will have the same problem.

The problem is with your table file, specifically the new line character. DOS uses \r\n , Mac \r and Linux \n.
Your text file uses \r, so it probably was created on a mac.

The problem is that the "cat" command (at least in linux) does not work on your file:
cat long.qdec.table.dat is empty

You can convert the \r to \n (linux format):
tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat

and then should be able to run the preproc command.

People with DOS formats should not run the above "tr' command as they will end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat' directly (so there is no need)? If anyone on the list knows a good way of cat and awk a file independently of the new line (and working on all OS), let me know. This is the command I use:

cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") printf("%s.long.%s\n", $1, $2)}'

to generate the subjects id's from the table's first two columns.

Best, Martin

On 06/03/2013 03:45 PM, Christopher McCarthy wrote:

Dr. Reuter,

We corresponded in the past about QDEC, and you gave me great help. The lab I work for is now moving towards using the Longitudinal Mixed Effects Model. When I go to run the command:

mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh

I get the error: 'ERROR: no subjects specified.' I am attaching my long.qdec.table.dat, which works fine when loaded by QDEC. Do you have any idea of why I am getting this error?

Thanks,

Chris McCarthy

--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
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Charlestown, MA 02129

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