Hi @effigies and Peer
Thanks for the feedback.
Unfortunately I don’t have the entire log (it doesn’t give me all of the history), but below is the initiating log (first line etc.)
I have also modified my bash script and will try that today.
RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=18.09.7 -v /usr/local/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /home/lara/Documents/Lara/CM/cm_mri/Session2/Input:/data:ro -v /home/lara/Documents/Lara/CM/cm_mri/Session2/Output:/out poldracklab/fmriprep:1.4.0 /data /out participant --participant_label=sub-15 -vvv --use-aroma --write-graph --stop-on-first-crash --ignore=fieldmaps
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
1: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a “.bidsignore” file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)
Please visit https://neurostars.org/search?q=NOT_INCLUDED for existing conversations about this issue.
2: [ERR] Dataset does not contain any T1w scans. (code: 53 - NO_T1W)
Please visit https://neurostars.org/search?q=NO_T1W for existing conversations about this issue.
3: [ERR] Subject label in the filename doesn't match with the path of the file. File seems to be saved in incorrect subject directory. (code: 64 - SUBJECT_LABEL_IN_FILENAME_DOESNOT_MATCH_DIRECTORY)
Evidence: File: /sub-15/session2/anat/sub-69_T1w.json is saved in incorrect subject directory as per sub-id in filename.
Evidence: File: /sub-15/session2/anat/sub-69_T1w.nii.gz is saved in incorrect subject directory as per sub-id in filename.
Evidence: File: /sub-15/session2/fmap/sub-69_magnitude1.nii.gz is saved in incorrect subject directory as per sub-id in filename.
Evidence: File: /sub-15/session2/fmap/sub-69_phasediff.json is saved in incorrect subject directory as per sub-id in filename.
Evidence: File: /sub-15/session2/fmap/sub-69_phasediff.nii.gz is saved in incorrect subject directory as per sub-id in filename.
Evidence: File: /sub-15/session2/func/sub-69_task-rest_bold.json is saved in incorrect subject directory as per sub-id in filename.
Evidence: File: /sub-15/session2/func/sub-69_task-rest_bold.nii.gz is saved in incorrect subject directory as per sub-id in filename.
Please visit https://neurostars.org/search?q=SUBJECT_LABEL_IN_FILENAME_DOESNOT_MATCH_DIRECTORY for existing conversations about this issue.
4: [ERR] No BIDS compatible data found for at least one subject. (code: 67 - NO_VALID_DATA_FOUND_FOR_SUBJECT)
... and 19 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=NO_VALID_DATA_FOUND_FOR_SUBJECT for existing conversations about this issue.
1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
401 Files, 1.5GB
0 - Subjects
1 - Session
If you have any questions, please post on https://neurostars.org/tags/bids.
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/multiprocessing/process.py”, line 297, in _bootstrap
File “/usr/local/miniconda/lib/python3.7/multiprocessing/process.py”, line 99, in run
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 445, in build_workflow
from …workflows.base import init_fmriprep_wf
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py”, line 25, in
from niworkflows.interfaces.bids import (
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/init.py”, line 6, in
from .confounds import ExpandModel, SpikeRegressors
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/confounds.py”, line 11, in
import pandas as pd
File “/usr/local/miniconda/lib/python3.7/site-packages/pandas/init.py”, line 42, in
from pandas.core.api import *
File “/usr/local/miniconda/lib/python3.7/site-packages/pandas/core/api.py”, line 10, in
from pandas.core.groupby.groupby import Grouper
File “/usr/local/miniconda/lib/python3.7/site-packages/pandas/core/groupby/init.py”, line 2, in
from pandas.core.groupby.groupby import (
File “/usr/local/miniconda/lib/python3.7/site-packages/pandas/core/groupby/groupby.py”, line 46, in
from pandas.core.index import (Index, MultiIndex,
File “/usr/local/miniconda/lib/python3.7/site-packages/pandas/core/index.py”, line 2, in
from pandas.core.indexes.api import *
File “/usr/local/miniconda/lib/python3.7/site-packages/pandas/core/indexes/api.py”, line 4, in
from pandas.core.indexes.base import (Index,
File “”, line 983, in _find_and_load
File “”, line 967, in _find_and_load_unlocked
File “”, line 677, in _load_unlocked
File “”, line 724, in exec_module
File “”, line 857, in get_code
File “”, line 525, in _compile_bytecode
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 10, in
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 340, in main
File “/usr/local/miniconda/lib/python3.7/multiprocessing/process.py”, line 140, in join
res = self._popen.wait(timeout)
File “/usr/local/miniconda/lib/python3.7/multiprocessing/popen_fork.py”, line 48, in wait
return self.poll(os.WNOHANG if timeout == 0.0 else 0)
File “/usr/local/miniconda/lib/python3.7/multiprocessing/popen_forkserver.py”, line 61, in poll
if not wait([self.sentinel], timeout):
File “/usr/local/miniconda/lib/python3.7/multiprocessing/connection.py”, line 920, in wait
ready = selector.select(timeout)
File “/usr/local/miniconda/lib/python3.7/selectors.py”, line 415, in select
fd_event_list = self._selector.poll(timeout)
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fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issues