Gotcha, Thanks.
-----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Sent: Monday, May 20, 2013 10:06 AM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem
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
endif296c296
< set dcmfile = $b0mfile
set dcmfile = $dcmroot/$b0mfile311c311
< set dcmfile = $b0pfile
set dcmfile = $dcmroot/$b0pfileBut 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:ayendiki@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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