Re: [Freesurfer] mris_preproc --qdec-long problem

Hi Chris,

still the same (kind of) problem. For some reason you are getting an empty line in the qdec table so it expands the name to ".long." . Open your long.qdec.table.dat in an editor (e.g. nedit or gedit), maybe try to copy it into a new editor window, safe it and hope the editor fixes the problem. Also try cat ./qdec/long.qdec.table.dat to see what it prints, there should be no empty lines.

You can also use hexdump -cb ./qdec/long.qdec.table.dat to take a look at the files content, there should be single \n at the end of each line.

Best, Martin

On 06/04/2013 01:41 PM, Christopher McCarthy wrote:

Dr. Reuter,

Thanks for your help, it got me through the error I was having. On to the next one:

When I enter the command:

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

it spits out the following two lines before quitting:

nsubjects = 45 ERROR: cannot find /media/freesurfer/.long.

Any idea what I'm missing?

Thanks for your help and patience,

Chris

On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto: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
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652 <tel:%2B1-617-724-5652>
Email:
mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>
reuter@mit.edu <mailto:reuter@mit.edu>
Web  : http://reuter.mit.edu



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