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nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
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Mindboggle runtime error #197

Closed xiaoninh closed 3 years ago

xiaoninh commented 4 years ago

Hi, I am trying to do a test run using the one line command with the T1 image from the example input data. After almost 30 hours of running, I got an runtime error as followed:

Traceback (most recent call last): File "/opt/miniconda-latest/envs/mb/bin/mindboggle123", line 408, in mbFlow.run(plugin=args.plugin) File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py", line 595, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 61, in run report_nodes_not_run(notrun) File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/tools.py", line 82, in report_nodes_not_run raise RuntimeError(('Workflow did not execute cleanly. ')) RuntimeError: Workflow did not execute cleanly.

and I looked into the freesurfer_subjects/TEST_ID/scripts/recon-all.log, it has this error:

ERROR: FreeSurfer license file /opt/freesurfer-6.0.0-min/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

PeerHerholz commented 4 years ago

Issue is discussed in this neurostars thread.