Hi, so when I uploaded my dataset in the bids-validator, I got the above error, with more details as “We were unable to parse header data from this NIfTI file. Please ensure it is not corrupted or mislabeled”.
The nifti file is saved as this “HCP_DATA/sub-103818/dwi/sub-103818_acq-multishell_dwi.nii.gz”
However, when I ran this using the command line version, it didn’t show me this error.
Also, there was a dataset which has been made BIDS-compatible by my senior and I had replicated the same structure. However for her case, it didn’t show this error either in the web-version or the command line version. Is there any error in my data?
It seems to be a bug or an over-interpretation of the new release of BIDS validator, I got the same error on my data even though the nifty files are perfectly readable by FSL for instance. I moved on to try with an earlier version of the BIDS validator (v1.9.3) and didn’t get this error.
bids-validator /Volumes/data/MRI_BIDS_DATABANK_TEMP/Interception
bids-validator@1.9.8
(node:91361) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
1: [WARN] Task scans should have a corresponding events.tsv file. If this is a resting state scan you can ignore this warning or rename the task to include the word "rest". (code: 25 - EVENTS_TSV_MISSING)
./sub-3T001/func/sub-3T001_task-InterceptionPhase1_bold.nii.gz
./sub-3T001/func/sub-3T001_task-InterceptionPhase2_bold.nii.gz
./sub-3T001/func/sub-3T001_task-InterceptionPhase3_bold.nii.gz
./sub-3T001/func/sub-3T001_task-InterceptionPhase4_bold.nii.gz
./sub-3T002/func/sub-3T002_task-InterceptionPhase1_bold.nii.gz
./sub-3T002/func/sub-3T002_task-InterceptionPhase2_bold.nii.gz
./sub-3T002/func/sub-3T002_task-InterceptionPhase3_bold.nii.gz
./sub-3T002/func/sub-3T002_task-InterceptionPhase4_bold.nii.gz
./sub-3T003/func/sub-3T003_task-InterceptionPhase1_bold.nii.gz
./sub-3T003/func/sub-3T003_task-InterceptionPhase2_bold.nii.gz
... and 6 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=EVENTS_TSV_MISSING for existing conversations about this issue.
2: [WARN] Not all subjects contain the same files. Each subject should contain the same number of files with the same naming unless some files are known to be missing. (code: 38 - INCONSISTENT_SUBJECTS)
./sub-3T001/func/sub-3T001_task-InterceptionPhase1_recording-cardiac_physio.json
Evidence: Subject: sub-3T001; Missing file: sub-3T001_task-InterceptionPhase1_recording-cardiac_physio.json
./sub-3T001/func/sub-3T001_task-InterceptionPhase1_recording-cardiac_physio.tsv.gz
Evidence: Subject: sub-3T001; Missing file: sub-3T001_task-InterceptionPhase1_recording-cardiac_physio.tsv.gz
./sub-3T001/func/sub-3T001_task-InterceptionPhase2_recording-cardiac_physio.json
Evidence: Subject: sub-3T001; Missing file: sub-3T001_task-InterceptionPhase2_recording-cardiac_physio.json
./sub-3T001/func/sub-3T001_task-InterceptionPhase2_recording-cardiac_physio.tsv.gz
Evidence: Subject: sub-3T001; Missing file: sub-3T001_task-InterceptionPhase2_recording-cardiac_physio.tsv.gz
./sub-3T001/func/sub-3T001_task-InterceptionPhase2_recording-respiratory_physio.json
Evidence: Subject: sub-3T001; Missing file: sub-3T001_task-InterceptionPhase2_recording-respiratory_physio.json
./sub-3T001/func/sub-3T001_task-InterceptionPhase2_recording-respiratory_physio.tsv.gz
Evidence: Subject: sub-3T001; Missing file: sub-3T001_task-InterceptionPhase2_recording-respiratory_physio.tsv.gz
./sub-3T001/func/sub-3T001_task-InterceptionPhase3_recording-cardiac_physio.json
Evidence: Subject: sub-3T001; Missing file: sub-3T001_task-InterceptionPhase3_recording-cardiac_physio.json
./sub-3T001/func/sub-3T001_task-InterceptionPhase3_recording-cardiac_physio.tsv.gz
Evidence: Subject: sub-3T001; Missing file: sub-3T001_task-InterceptionPhase3_recording-cardiac_physio.tsv.gz
./sub-3T001/func/sub-3T001_task-InterceptionPhase3_recording-respiratory_physio.json
Evidence: Subject: sub-3T001; Missing file: sub-3T001_task-InterceptionPhase3_recording-respiratory_physio.json
./sub-3T001/func/sub-3T001_task-InterceptionPhase3_recording-respiratory_physio.tsv.gz
Evidence: Subject: sub-3T001; Missing file: sub-3T001_task-InterceptionPhase3_recording-respiratory_physio.tsv.gz
... and 10 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=INCONSISTENT_SUBJECTS for existing conversations about this issue.
3: [WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)
./sub-3T001/fmap/sub-3T001_dir-AP_epi.nii.gz
./sub-3T001/fmap/sub-3T001_dir-PA_epi.nii.gz
./sub-3T002/anat/sub-3T002_acq-csmp2rage_inv-1_part-mag_MP2RAGE.nii.gz
Please visit https://neurostars.org/search?q=INCONSISTENT_PARAMETERS for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
192 Files, 12.52GB InterceptionPhase1 MRI
4 - Subjects InterceptionPhase2
1 - Session InterceptionPhase3
InterceptionPhase4
If you have any questions, please post on https://neurostars.org/tags/bids.
There are is a limited library of helper functions written in Python. The main function determines if a file extension is compliant with the BIDS specification.
@meka Your issue (may or may not be the same as above) is that large header extensions that extend the header beyond 1024 bytes of compressed data. I’ll open an issue on the validator and we can get this fixed this week.