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beOn / hcpre

A Nipype Workflow for the HCP Preprocessing Pipelines
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Location of Caret7 install option #1

Closed ito-takuya closed 10 years ago

ito-takuya commented 10 years ago

It looks like the caret7 install is automatically pointing to the binaries within the HCP pipeline install (i.e., ${HCPPIPEDIR}/global/binaries/caret7/bin_rh_linux64/), but since I'm running on a Mac server, we're using workbench from a different directory (hopefully using the Mac version of workbench won't cause any problems, but won't know). I'm not sure where the caret7 path is set in the workflow, but I assume it might be more on the HCP pipeline side, rather than the hcpre side.

My binary equivalent for workbench are located in /Applications/workbench/bin_macosx64

ito-takuya commented 10 years ago

Update: I tried to 'hack' it a bit, and changed my HCP pipeline caret7 install with the following changes: I changed the file: ${HCPPIPEDIR}/global/binaries/caret7/bin_rh_linux64/wb_command where the last two lines were previously ########### echo "$LD_LIBRARY_PATH"

"$directory"/../exe_rh_linux64/wb_command "$@" ############# and changed to: ############ echo "$LD_LIBRARY_PATH"

/Applications/workbench/macosx64_apps/wb_command.app/Contents/MacOS/wb_command "$@" ################

For some reason, this got the previous error to work (it previously broke at PreFS with the unwarp command), and now it's breaking at the PostFS interface. Haven't looked through the error output in detail yet, but at first glance, it looks as though it might be a problem with the mac version of workbench.

ito-takuya commented 10 years ago

Here are the actual error outputs, if you have any insights on them... Looks like workbench on mac might not be compatible with caret7 install on hcp pipeline, though I'm not familiar with caret or workbench.

reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ERROR, Command Failed: the switch '-gifti-label-add-prefix' does not match any processing commands

Return code: 255 Interface PostFS failed to run.

140516-04:26:06,838 workflow INFO:

140516-04:26:06,838 workflow ERROR: could not run node: hcp_prep_workflow.post_freesurfer.a0 140516-04:26:06,838 workflow INFO: crashfile: /projects/BlockRepPRO/scripts/crash-20140516-042604-taku.ito-post_freesurfer.a0.npz 140516-04:26:06,838 workflow INFO:

Traceback (most recent call last): File "/usr/bin/anaconda/bin/hcpipe.py", line 176, in sys.exit(main()) File "/usr/bin/anaconda/bin/hcpipe.py", line 163, in main wk.run(plugin="MultiProc", plugin_args={"n_procs" : N_PROCS, "non_daemon" : True}) File "/usr/bin/anaconda/lib/python2.7/site-packages/hcpre/workflows.py", line 84, in run super(HCPrepWorkflow, self).run(_args, *_kwargs) File "/usr/bin/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 689, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/usr/bin/anaconda/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 262, in run report_nodes_not_run(notrun) File "/usr/bin/anaconda/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 90, in report_nodes_not_run raise RuntimeError(('Workflow did not execute cleanly. ' RuntimeError: Workflow did not execute cleanly. Check log for details

beOn commented 10 years ago

fixed in https://github.com/beOn/hcpre/commit/2e014e42d5429bfa5328b3140f9eebdcc60f2e03