I am getting the following output with error on this command:


trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23


INFO: SUBJECTS_DIR is /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: /home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected


I apologize for not finding the answer in the list archive.

It's probably there.


I'm running under ubuntu 14.04.


bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:


INFO: SUBJECTS_DIR is /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
subjectdir is /media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
Making bedpostx directory structure
Queuing preprocessing stages
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: /home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected (expecting ";;")
Queuing parallel processing stage
0 slices processed
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: /home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected (expecting ";;")
Queuing post processing stage
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: /home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected (expecting ";;")
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: line 439: 26461 Terminated              ${subjdir}.bedpostX/monitor


Thanks - Don