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nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
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"Shape_tables.a1 failed to run on host" error running on mindboggle_input_example #188

Closed jling-NM closed 4 years ago

jling-NM commented 4 years ago

Downloaded docker container 10/4/2019. Downloaded mindboggle_input_example.zip and expanded to home directory.

Ran these commands: CLI:

HOST=/home/jling DOCK=/home/jovyan/work docker run --rm -ti -v $HOST:$DOCK -p 5000:5000 nipy/mindboggle

DOCKER CLI: root@95c8ebfc8045:/# DOCK=/home/jovyan/work EXAMPLE=$DOCK/mindboggle_input_example FREESURFER_SUBJECT=$EXAMPLE/freesurfer/subjects/arno ANTS_SUBJECT=$EXAMPLE/ants/subjects/arno OUT=$DOCK/mindboggled mindboggle $FREESURFER_SUBJECT --out $OUT --roygbiv --ants $ANTS_SUBJECT/antsBrainSegmentation.nii.gz --no_volumes --no_sulci --no_moments --no_spectra

Always fails at Shape_tables: 191007-21:44:55,399 nipype.workflow INFO: [Node] Setting-up "Mindboggle.Shape_tables" in "/home/jovyan/work/mindboggled/working/arno/Mindboggle/_hemi_rh/Shape_tables". 191007-21:44:55,860 nipype.workflow INFO: [Node] Running "Shape_tables" ("nipype.interfaces.utility.wrappers.Function") 191007-21:46:04,985 nipype.workflow ERROR: Node Shape_tables.a1 failed to run on host 95c8ebfc8045. 191007-21:46:04,987 nipype.workflow ERROR: Saving crash info to /opt/crash-20191007-214604-root-Shape_tables.a1-a3ba1825-c9f0-48df-8e48-e29dd9d1afa7.txt Traceback (most recent call last): File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run node.run(updatehash=updatehash) File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 493, in run write_node_report(self, result=result, is_mapnode=isinstance(self, MapNode)) File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 214, in write_node_report report_file.write_text('\n'.join(lines)) File "/opt/miniconda-latest/envs/mb/lib/python3.6/pathlib.py", line 1216, in write_text return f.write(data) UnicodeEncodeError: 'ascii' codec can't encode character '\u2019' in position 1717: ordinal not in range(128)

jling-NM commented 4 years ago

After reviewing issue #175 and the June 11th announcement. i believe issue #175 may have returned or I'm not getting a recent image from docker hub.

jling-NM commented 4 years ago

I went to a different docker host, downloaded everything again and it works.

locta66 commented 4 years ago

I went to a different docker host, downloaded everything again and it works.

I have the same problem, even if I change my docker host and pull again. Which docker host do you use?