Hi Don - See:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html
Best,
a.y
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Krieger, Donald N.
<krieg...@upmc.edu>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question
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
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