Hi,
I just updated my fmriprep singularity image to version 1.3.0.post2. I attempted to process some data but the program crashed pretty quickly. I’ve pasted the output log below. Do you know what the issue might be?
Thanks very much
This dataset appears to be BIDS compatible.
Summary: Available Tasks: Available Modalities:
218784 Files, 75.42GB cardguess T1w
20 - Subjects rest bold
1 - Session lapse fieldmap
If you have any questions please post on https://neurostars.org/tags/bids
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __pa
th__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __pa
th__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __pa
th__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __pa
th__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of fr
om 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/datalad/utils.py:71: DeprecationWarning: dist() and linux_distribution() functions are deprecated in Python 3.5
= platform.linux_distribution()[:2]
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 560, in build_workflow
from ..workflows.base import init_fmriprep_wf
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 24, in <module>
from niworkflows.interfaces.bids import (
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/__init__.py", line 8, in <module>
from .registration import (FLIRTRPT as FLIRT,
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/registration.py", line 25, in <module>
from .mni import (
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/mni.py", line 20, in <module>
from templateflow.api import get as get_template
File "/usr/local/miniconda/lib/python3.7/site-packages/templateflow/api.py", line 5, in <module>
from datalad import api
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/__init__.py", line 31, in <module>
cfg = ConfigManager()
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/config.py", line 204, in __init__
self.reload(force=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/config.py", line 258, in reload
stdout, stderr = self._run(run_args, log_stderr=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/config.py", line 526, in _run
out = self._runner.run(['git', 'config'] + args, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/cmd.py", line 670, in run
cmd, env=self.get_git_environ_adjusted(env), *args, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/cmd.py", line 530, in run
raise CommandError(str(cmd), msg, status, out[0], out[1])
datalad.support.exceptions.CommandError: CommandError: command '['git', 'config', '-z', '-l']' failed with exitcode 127
Failed to run ['git', 'config', '-z', '-l'] under None. Exit code=127. out= err=FATAL: kernel too old