Hello,
I am using fmriprep 21.0.0 and its docker wrapper on a linux workstation to process ~200 subjects with multi-echo resting-state data. The data lives on a network server but the processing is done by the workstation not a HPC. I created a separate test bids directory with one subject and successfully processed their data through fmriprep. Using the same command on the path to the actual directory but still only one subject led fmriprep to hang after printing the docker command but no other outputs. I believe it appears to hang because of the pybids indexing. So, I pre-indexed following the FAQ and added the flag + path --bids-database-dir to the wrapper command. Unfortunately, that raises an error about the root directory not existing. I then replicated the error on the test directory. Permissions and memory seem fine and the root path is definitely correct and bids compliant. Any thoughts on what is the issue?
Commands
pybids layout $bids_root_dir $pybids_dir --no-validate --index-metadata
fmriprep-docker $bids_root_dir \
$bids_deriv_dir \
participant \
--participant-label $subj \
--skip-bids-validation \
--bids-database-dir $pybids_dir \
--md-only-boilerplate \
--fs-license-file $FS_LICENSE \
--fs-no-reconall \
--output-spaces T1w \
--ignore slicetiming fieldmaps sbref t2w flair \
--dummy-scans 4 \
--skull-strip-t1w force \
--fs-subjects-dir $fs_dir$subj \
--me-output-echos \
--stop-on-first-crash \
--low-mem \
-u $(id -u):$(id -g)
Output
collhugh@albany:/lbc/lbc1/PREVENT_AD/derivatives/rsFC/rsFC_fmriprep$ ./code/docker_PAD.sh
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.7 -it -u 3095:1086 -v /lbc/lbc1/PREVENT_AD/derivatives/rsFC/rsFC_fmriprep/license.txt:/opt/freesurfer/license.txt:ro -v /lbc/lbc1/PREVENT_AD/PREVENT_AD_BIDS:/data:ro -v /lbc/lbc1/PREVENT_AD/derivatives/rsFC/rsFC_fmriprep/derivatives:/out -v /lbc/lbc1/PREVENT_AD/derivatives/freesurfer/sub-0196:/opt/subjects -v /lbc/lbc1/PREVENT_AD/derivatives/rsFC/pybids_db:/tmp/bids_db nipreps/fmriprep:21.0.0 /data /out participant --participant-label 0196 --skip-bids-validation --md-only-boilerplate --fs-no-reconall --ignore slicetiming fieldmaps sbref t2w flair --dummy-scans 4 --skull-strip-t1w force --me-output-echos --stop-on-first-crash --low-mem --fs-subjects-dir /opt/subjects --bids-database-dir /tmp/bids_db --output-spaces T1w
/opt/conda/lib/python3.8/site-packages/bids/config.py:39: FutureWarning: Setting βextension_initial_dotβ will be removed in pybids 0.16.
warnings.warn(βSetting βextension_initial_dotβ will be removed in pybids 0.16.β,
Traceback (most recent call last):
File β/opt/conda/bin/fmriprepβ, line 8, in
sys.exit(main())
File β/opt/conda/lib/python3.8/site-packages/fmriprep/cli/run.pyβ, line 38, in main
parse_args()
File β/opt/conda/lib/python3.8/site-packages/fmriprep/cli/parser.pyβ, line 668, in parse_args
config.from_dict(vars(opts))
File β/opt/conda/lib/python3.8/site-packages/fmriprep/config.pyβ, line 664, in from_dict
execution.load(settings)
File β/opt/conda/lib/python3.8/site-packages/fmriprep/config.pyβ, line 238, in load
cls.init()
File β/opt/conda/lib/python3.8/site-packages/fmriprep/config.pyβ, line 481, in init
cls._layout = BIDSLayout(
File β/opt/conda/lib/python3.8/site-packages/bids/layout/layout.pyβ, line 126, in init
root, description = validate_root(root, validate)
File β/opt/conda/lib/python3.8/site-packages/bids/layout/validation.pyβ, line 68, in validate_root
raise ValueError(βBIDS root does not exist: %sβ % root)
ValueError: BIDS root does not exist: /lbc/lbc1/PREVENT_AD/PREVENT_AD_BIDS
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues