Summary of what happened:
Hello:
I’ve decided to ditch my Mac M2 desktop because of compatibility issues. No solution to the errors and the extremely long times (>20h without FS) to never complete. I’m now working on a Linux machine running Ubuntu. Some permissions issues keep coming up. First, I have to add sudo before the command.
Second, the temporary folders it creates inside my workingFolder are locked and owned by the root rather than the user. I am trying to figure our how to make it so that whatever is created is not locked. Hopefully, also avoid having to add sudo before the code. I’m concerned it will cause issues down the line.
Also, it returns an error saying that ‘dataset_description.json’ is missing from project root. But it is in my BIDS folder.
In my BIDS folder I have
- code
- derivatives
- raw
- fsl-license
- workingFolder
dataset_description.json
participants.json
participant.tsv
Any ideas on what is causing this? I was hoping that transitioning to Linux would solve my problems but it doesn’t seem so… I would really want to use fMRIprep but will have to ditch it if I can’t promptly start analyzing my data.
Command used (and if a helper script was used, a link to the helper script or the command generated):
sudo fmriprep-docker \
/home/nens/Desktop/BIDS/raw \
/home/nens/Desktop/BIDS/derivatives \
participant --participant-label sub-007 \
--fs-license-file /home/nens/Desktop/BIDS/fsl_license/license.txt \
--skip-bids-validation \
--dummy-scans 1 \
--output-spaces MNI152NLin2009cAsym:res-2 \
-w /home/nens/Desktop/BIDS/workingFolder
Version:
fmriprep:23.2.1
Environment (Docker, Singularity / Apptainer, custom installation):
Docker on Ubuntu
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Terminal output (no log file saved)
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=24.0.5 -it -v /home/nens/Desktop/BIDS/fsl_license/license.txt:/opt/freesurfer/license.txt:ro -v /home/nens/Desktop/BIDS/raw:/data:ro -v /home/nens/Desktop/BIDS/derivatives:/out -v /home/nens/Desktop/BIDS/workingFolder:/scratch nipreps/fmriprep:23.2.1 /data /out participant --participant-label sub-007 --skip-bids-validation --dummy-scans 1 -w /scratch --output-spaces MNI152NLin2009cAsym:res-2
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/python3.10/site-packages/fmriprep/cli/run.py", line 40, in main
parse_args()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/parser.py", line 802, in parse_args
config.from_dict({})
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/config.py", line 691, in from_dict
execution.load(settings, init=initialize('execution'), ignore=ignore)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/config.py", line 235, in load
cls.init()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/config.py", line 485, in init
cls._layout = BIDSLayout(
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/layout.py", line 135, in __init__
root, description = validate_root(root, validate)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/validation.py", line 75, in validate_root
raise BIDSValidationError(
bids.exceptions.BIDSValidationError: 'dataset_description.json' is missing from project root. Every valid BIDS dataset must have this file.
Screenshots / relevant information:
