Hi Matt - Yes, the dcmroot variable can be used if you have the same root
directory for *all* input files. If not, don't define dcmroot and instead
give the full path to each input file. Then you shouldn't have to modify
any scrips.
a.y
On Fri, 17 May 2013, Hoptman, Matthew wrote:
Hi Anastasia,
I solved this particular problem in a new dmrirc, but it seemed that I had to
modify trac-all 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:ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 12:31 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
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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