Hi Salil - It's a well-known (see email archives) compatibility issue with the newer version of bedpostx, that has different command-line arguments than it used to. You can run bedpostx directly on the command line for now. This is solved in the next version of trac-all.
a.y
On Sat, 19 Jan 2013, Salil Soman wrote:
Dear Freesurfer Experts,
I am running freesurfer (centos4 64 bit v5.10) and a fsl 5.0.2.1 (compiled from source code) on a cluster running ubuntu 12.04 and the debian version of sun grid engine. I have successfully run freesurfer and trac-all -prep using this configuration. However, when I try to run trac-all -bedp -c dmrirc_file, the process I get the following progress and abrupt termination within a hour or so:
ln -sf/mnt/glusterfs/myaccount/output/TRACULA/CRP_FS/dlabel/diff/aparc+aseg_mask. bbr.nii.gz /mnt/glusterfs/myaccount/output/TRACULA/$ ln -sf /mnt/glusterfs/myaccount/output/TRACULA/CRP_FS/dmri/dwi.nii.gz /mnt/glusterfs/myaccount/output/TRACULA/CRP_FS/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /mnt/glusterfs/myaccount/output/TRACULA/CRP_FS/dmri subjectdir is /mnt/glusterfs/myaccount/output/TRACULA/CRP_FS/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed 1 slices processed 1 slices processed 1 slices processed 1 slices processed 1 slices processed 1 slices processed 1 slices processed 1 slices processed Queuing post processing stage
/mnt/glusterfs/myaccount/freesurfer/bin/bedpostx_seychelles: line 376: 14275 Terminated ${subjdir}.bedpostX/monitor
Any suggestions on what I am doing incorrectly?
Thank you,
Salil Soman, MD, MS