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
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
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.
Does anyone have the same problem or have the solution for it?