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Maybe the problem with #2409 is just nipype + Python 3.8+.

mgxd and others added 11 commits May 13, 2021 19:56
This PR bumps up the Docker image base to Ubuntu Focal LTS (20.04).

As a result, a number of packages were updated, including:
- AFNI
- FSL
- Connectome Workbench
- Graphviz
- Pandoc

Furthermore, Python was bumped to 3.8.x, and many of its packages were "modernized" accordingly.
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@mgxd
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mgxd commented Jun 16, 2021

I wonder if this is the same segfault

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 434, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/fsl/preprocess.py", line 164, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 760, in raise_exception
    ).format(**runtime.dictcopy())
RuntimeError: Command:
bet /scratch/fmriprep_wf/single_subject_100185_wf/func_preproc_task_machinegame_run_02_wf/initial_boldref_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_sbref_corrected.nii.gz /scratch/fmriprep_wf/single_subject_100185_wf/func_preproc_task_machinegame_run_02_wf/initial_boldref_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_sbref_corrected_brain.nii.gz -f 0.20 -m
Standard output:

Standard error:
Segmentation fault (core dumped)
Return code: 0

@effigies
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That would be a relief. Shall we revert FSL for now?

@mgxd
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mgxd commented Jun 16, 2021

i'd like to test locally first, but if it ends up being complicated i'm fine with downgrading.

@effigies
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Well, these are just experiments, so I'll see if that's the root of it. Won't merge anything.

@effigies
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Another option: Can we try FSL 6, if we're using neurodocker builds?

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mgxd commented Jun 21, 2021

this can be closed since #2409 is in

@mgxd mgxd closed this Jun 21, 2021
@effigies effigies deleted the enh/py37 branch August 24, 2023 03:40
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2 participants