Summary of what happened:
The readme file is created as an empty file of 0kb, and fmriprep does not run.
Even though it was configured using the dcm2bids_scaffold command, the readme file is 0kb.
1: [ERR] Empty files not allowed. (code: 99 - EMPTY_FILE)
./README
Command used (and if a helper script was used, a link to the helper script or the command generated):
dcm2bids_scaffold -o /mnt/d/test11
fmriprep-docker d:\test11 d:\test11\derivatives --fs-license-file d:\freesurfer.txt --nprocs 24 --omp-nthreads 12
Version:
dcm2bids version: 3.2.0
Based on BIDS version: v1.9.0
fMRIPrep v24.0.1
Environment (Docker, Singularity / Apptainer, custom installation):
dcm2bids: ubuntu - conda
fmriprep: docker
Data formatted according to a validatable standard? Please provide the output of the validator:
PS C:\Users\user> bids-validator d:/test11
bids-validator@1.14.8
(node:42384) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
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.
2: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)
Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.
3: [WARN] The Name field of dataset_description.json is present but empty of visible characters. (code: 115 - EMPTY_DATASET_NAME)
Please visit https://neurostars.org/search?q=EMPTY_DATASET_NAME for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
46 Files, 499.49MB rest MRI
3 - Subjects
1 - Session
If you have any questions, please post on https://neurostars.org/tags/bids.
Relevant log outputs (up to 20 lines):
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=27.1.1 -it -v d:\freesurfer.txt:/opt/freesurfer/license.txt:ro -v d:\test11:/data:ro -v d:\test11\derivatives:/out nipreps/fmriprep:24.0.1 /data /out participant --nprocs 24 --omp-nthreads 12
You are using fMRIPrep-24.0.1, and a newer version of fMRIPrep is available: 24.1.1.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
bids-validator@1.14.6
(node:9) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
1: [ERR] Empty files not allowed. (code: 99 - EMPTY_FILE)
./README
Please visit https://neurostars.org/search?q=EMPTY_FILE for existing conversations about this issue.
1: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)
Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.
2: [WARN] The Name field of dataset_description.json is present but empty of visible characters. (code: 115 - EMPTY_DATASET_NAME)
Please visit https://neurostars.org/search?q=EMPTY_DATASET_NAME for existing conversations about this issue.
3: [WARN] The recommended file /README is very small. Please consider expanding it with additional information about the dataset. (code: 213 - README_FILE_SMALL)
./README
Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
47 Files, 499.49MB rest MRI
3 - Subjects
1 - Session
If you have any questions, please post on https://neurostars.org/tags/bids.
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/bin/fmriprep", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/cli/run.py", line 40, in main
parse_args()
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/cli/parser.py", line 903, in parse_args
validate_input_dir(
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/utils/bids.py", line 245, in validate_input_dir
subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name]) # noqa: S607
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bids-validator', '/data', '-c', '/tmp/tmp6err41_i.json']' returned non-zero exit status 1.
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues
Screenshots / relevant information:
