I’m using the recent 1.3.0.post2 singularity image built with singularity build fmriprep-1.3.0.simg docker://poldracklab/fmriprep:latest, and still getting an error related to datalad and git configuration (below). Never seen this with previous versions of fmriprep, I just pulled a new container today. Mounting the TemplateFlow folder with -B $HOME/templateflow:/opt/templateflow doesn’t help. Git version inside the container is 2.7.4, and the kernel release in the container is 2.6.32-696.18.7.el6.x86_64.
@effigies suggested that it was a libc/kernel mismatch (just quoting, not sure I understand the cogs of this problem that well).
Full traceback:
/data/jux/mackey_group/public_data/ABCD/bids_fast_track_site14/
This dataset appears to be BIDS compatible.
Summary: Available Tasks: Available Modalities:
36430 Files, 296.59GB rest /participants
139 - Subjects T1w
1 - Session bold
events
scans
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 __path__
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 __path__
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 __path__
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 __path__
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 from '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