[snray@merida] $ singularity run --cleanenv /data/ucsfocd/software/fmriprep-23.1.4.simg /data/ucsfocd/data/mri/SEEG_subjects/nifti/rawdata /data/ucsfocd/data/mri/SEEG_subjects/nifti/derivatives/fmriprep-23.1.4 participant --participant-label SEEG02 -w /working/brain1/brain_work2/snray --fs-license-file /home/snray/Documents/freesurfer_license_sr.txt --output-spaces T1w MNI152NLin6Asym:res-2 fsaverage5 fsLR:den-32k --nthreads 6 --omp-nthreads 3 --verbose You are using fMRIPrep-23.1.4, and a newer version of fMRIPrep is available: 24.0.1. Please check out our documentation about how and when to upgrade: https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading 240923-13:58:22,425 cli INFO: Telemetry system to collect crashes and errors is enabled - thanks for your feedback!. Use option ``--notrack`` to opt out. 240923-13:58:27,531 cli INFO: Making sure the input data is BIDS compliant (warnings can be ignored in most cases). bids-validator@1.11.0 (node:8385) Warning: Closing directory handle on garbage collection (Use `node --trace-warnings ...` to show where the warning was created) 1: [ERR] 'IntendedFor' field needs to point to an existing file. (code: 37 - INTENDED_FOR) ./sub-SEEG02/ses-01/fmap/sub-SEEG02_ses-01_acq-pepolar_dir-AP_run-01_epi.nii.gz Evidence: ses-01/func/sub-SEEG02_ses-01_task-rest_acq-abcd_run-02_bold.nii.gz ./sub-SEEG02/ses-01/fmap/sub-SEEG02_ses-01_acq-pepolar_dir-AP_run-01_epi.nii.gz Evidence: ses-01/func/sub-SEEG02_ses-01_task-rest_acq-abcd_run-03_bold.nii.gz ./sub-SEEG02/ses-01/fmap/sub-SEEG02_ses-01_acq-pepolar_dir-AP_run-01_epi.nii.gz Evidence: ses-01/func/sub-SEEG02_ses-01_task-rest_acq-abcd_run-04_bold.nii.gz ./sub-SEEG02/ses-01/fmap/sub-SEEG02_ses-01_acq-pepolar_dir-AP_run-01_epi.nii.gz Evidence: ses-01/func/sub-SEEG02_ses-01_task-rest_acq-multiecho4_run-01_bold.nii.gz ./sub-SEEG02/ses-01/fmap/sub-SEEG02_ses-01_acq-pepolar_dir-AP_run-01_epi.nii.gz Evidence: ses-01/func/sub-SEEG02_ses-01_task-rest_acq-multiecho4_run-02_bold.nii.gz ./sub-SEEG02/ses-01/fmap/sub-SEEG02_ses-01_acq-pepolar_dir-AP_run-01_epi.nii.gz Evidence: ses-01/func/sub-SEEG02_ses-01_task-rest_acq-multiecho4_run-03_bold.nii.gz ./sub-SEEG02/ses-01/fmap/sub-SEEG02_ses-01_acq-pepolar_dir-AP_run-01_epi.nii.gz Evidence: ses-01/func/sub-SEEG02_ses-01_task-rest_acq-multiecho4_run-04_bold.nii.gz ./sub-SEEG02/ses-01/fmap/sub-SEEG02_ses-01_acq-pepolar_dir-AP_run-01_epi.nii.gz Evidence: ses-01/func/sub-SEEG02_ses-01_task-rest_acq-multiecho4_run-05_bold.nii.gz ./sub-SEEG02/ses-01/fmap/sub-SEEG02_ses-01_acq-pepolar_dir-AP_run-01_epi.nii.gz Evidence: ses-01/func/sub-SEEG02_ses-01_task-rest_acq-multiecho4_run-06_bold.nii.gz ./sub-SEEG02/ses-01/fmap/sub-SEEG02_ses-01_acq-pepolar_dir-AP_run-01_epi.nii.gz Evidence: ses-01/func/sub-SEEG02_ses-01_task-rest_acq-multiecho4_run-07_bold.nii.gz ... and 34 more files having this issue (Use --verbose to see them all). Please visit https://neurostars.org/search?q=INTENDED_FOR 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. 2: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered because there are no authors, which will make DOI registration from dataset metadata impossible. (code: 113 - NO_AUTHORS) Please visit https://neurostars.org/search?q=NO_AUTHORS for existing conversations about this issue. Summary: Available Tasks: Available Modalities: 167 Files, 5.13GB rest MRI 2 - 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 sys.exit(main()) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/run.py", line 43, in main parse_args() File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/parser.py", line 812, in parse_args validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/utils/bids.py", line 185, in validate_input_dir subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name]) File "/opt/conda/envs/fmriprep/lib/python3.10/subprocess.py", line 369, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['bids-validator', '/data/ucsfocd/data/mri/SEEG_subjects/nifti/rawdata', '-c', '/tmp/tmpmfknu9ga.json']' returned non-zero exit status 1. [snray@merida] $