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: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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