Hi Anastasia, I'm just forwarding a modified version of the email I'd sent you earlier to the list so everyone can see it.
I solved this particular problem in a new dmrirc, but it seemed that I had to
modify trac-preproc to remove the ${dcmroot} in front of:
infile, b0mfile and b0pfile:
diff bin/trac-preproc bin/trac-preproc.orig
< if ($#dcmroot > 0) set infile = $infile
---
> if ($#dcmroot > 0) set infile = $dcmroot/$infile
259c259
< endif
---
> endif
296c296
< set dcmfile = $b0mfile
---
> set dcmfile = $dcmroot/$b0mfile
311c311
< set dcmfile = $b0pfile
---
> set dcmfile = $dcmroot/$b0pfile
But now it doesn't seem to loop through the subjects, so I'm doing them one at
a time (painful).
Also, if, as in my other question, I try to run this as a cluster job, I don't
know how I can substitute a new subject into subjlist. I have 64 subjects and
would like to do trac-all -prep -c dmri on all of them simultaneously. I have
used bedpostx in SGE, but there you can just write loop to get it to go through
your subjects.
If I could make the subject variable external to dmrirc, I could do easily
script the trac-all job to run in SGE, but I can't fiugre out how to pass it to
the trac-all command. Is there any way to pass the subject number directly to
the command?
Does this make sense?
Matt
-----Original Message-----
From: Anastasia Yendiki [mailto:[email protected]]
Sent: Friday, May 17, 2013 12:31 PM
To: Hoptman, Matthew
Cc: [email protected]
Subject: Re: [Freesurfer] Tracula problem
Hi Matt - Can you source try this on the command line:
source dmrirc_53beta
echo $b0mlist
echo $b0plist
Are these filenames correct, do these files exist? This is how you define
them in your configuration file:
set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`)
set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`)
Thanks,
a.y
On Wed, 15 May 2013, Hoptman, Matthew wrote:
>
> Hi all,
>
>
>
> I’m having a problem with tracula. I’m trying to run in version 5.3 beta (is
> that
> version very different from the newer 5.3?). If I run
>
> trac-preproc -c dmrirc –prep,
>
>
> I get:
>
> mri_convert /home/hoptman/freesurfer/subjects/c159032/
> /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
>
> mri_convert /home/hoptman/freesurfer/subjects/c159032/
> /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
>
> corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info
>
>
>
> I don’t know why it would look for COR-.info in the subjects’ root directory.
> I’m
> attaching my dmrirc file in case that helps.
>
>
>
> Thanks,
> Matt
>
> Matthew J. Hoptman, PhD
> Research Scientist V
> Nathan S. Kline Institute for Psychiatric Research
>
> Research Associate Professor in Psychiatry
> NYU School of Medicine
>
>
>
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