Great - thanks. It's running. I see several warnings which I presume can be ignored: hostname: Name or service not known
Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Tuesday, April 10, 2018 4:24 PM To: freesurfer <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] newbie trac-all -bedp question 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Krieger, Donald N. <krieg...@upmc.edu<mailto: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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