Hello, bids experts,
I’m a novice to this BIDS format data structure. I’m trying to prepare data to run fmriprep. So, stuck in converting from DICOM to BIDS format. I have used mricroGL’s ‘dcm2niix’ to convert from DICOM to BIDS. The ‘dcm2niix’ doesn’t provide the participants .tsv and .json files.
The converted filenames are
‘t1_mprage_sag_2.nii.gz’ --> renamed as ‘sub-01_t1_mprage_sag_2.nii.gz’
‘ep2d_pace_Rest_2000TR_3.nii.gz’ --> renamed as ‘sub-03_ep2d_pace_Rest_2000TR_3.nii.gz’
The BIDS-validator output given below from the terminal:
bids-validator ‘/home/naren123/Desktop/trial-BIDS’
1: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a “.bidsignore” file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)
./sub-02/anat/sub-02_t1_mprage_sag_2.json
Evidence: sub-02_t1_mprage_sag_2.json
./sub-02/anat/sub-02_t1_mprage_sag_2.nii.gz
Evidence: sub-02_t1_mprage_sag_2.nii.gz
./sub-02/dwi/sub-02_ep2d_diff_mddw_20_16.bval
Evidence: sub-02_ep2d_diff_mddw_20_16.bval
./sub-02/dwi/sub-02_ep2d_diff_mddw_20_16.bvec
Evidence: sub-02_ep2d_diff_mddw_20_16.bvec
./sub-02/dwi/sub-02_ep2d_diff_mddw_20_16.json
Evidence: sub-02_ep2d_diff_mddw_20_16.json
./sub-02/dwi/sub-02_ep2d_diff_mddw_20_16.nii.gz
Evidence: sub-02_ep2d_diff_mddw_20_16.nii.gz
./sub-02/func/sub-02_ep2d_pace_Rest_2000TR_3.json
Evidence: sub-02_ep2d_pace_Rest_2000TR_3.json
./sub-02/func/sub-02_ep2d_pace_Rest_2000TR_3.nii.gz
Evidence: sub-02_ep2d_pace_Rest_2000TR_3.nii.gz
./sub-03/anat/sub-03_t1_mprage_sag_2.json
Evidence: sub-03_t1_mprage_sag_2.json
./sub-03/anat/sub-03_t1_mprage_sag_2.nii.gz
Evidence: sub-03_t1_mprage_sag_2.nii.gz
… and 6 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=NOT_INCLUDED for existing conversations about this issue.
2: [ERR] Sub label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec. (code: 62 - SUBJECT_VALUE_CONTAINS_ILLEGAL_CHARACTER)
./sub-02/anat/sub-02_t1_mprage_sag_2.json
Evidence: sub name contains illegal character:/sub-02/anat/sub-02_t1_mprage_sag_2.json
./sub-02/dwi/sub-02_ep2d_diff_mddw_20_16.bval
Evidence: sub name contains illegal character:/sub-02/dwi/sub-02_ep2d_diff_mddw_20_16.bval
./sub-02/dwi/sub-02_ep2d_diff_mddw_20_16.json
Evidence: sub name contains illegal character:/sub-02/dwi/sub-02_ep2d_diff_mddw_20_16.json
./sub-02/func/sub-02_ep2d_pace_Rest_2000TR_3.json
Evidence: sub name contains illegal character:/sub-02/func/sub-02_ep2d_pace_Rest_2000TR_3.json
./sub-03/anat/sub-03_t1_mprage_sag_2.json
Evidence: sub name contains illegal character:/sub-03/anat/sub-03_t1_mprage_sag_2.json
./sub-03/dwi/sub-03_ep2d_diff_mddw_20_16.bval
Evidence: sub name contains illegal character:/sub-03/dwi/sub-03_ep2d_diff_mddw_20_16.bval
./sub-03/dwi/sub-03_ep2d_diff_mddw_20_16.json
Evidence: sub name contains illegal character:/sub-03/dwi/sub-03_ep2d_diff_mddw_20_16.json
./sub-03/func/sub-03_ep2d_pace_Rest_2000TR_3.json
Evidence: sub name contains illegal character:/sub-03/func/sub-03_ep2d_pace_Rest_2000TR_3.json
Please visit https://neurostars.org/search?q=SUBJECT_VALUE_CONTAINS_ILLEGAL_CHARACTER for existing conversations about this issue.
3: [ERR] No BIDS compatible data found for at least one subject. (code: 67 - NO_VALID_DATA_FOUND_FOR_SUBJECT)
./sub-02
./sub-03
Please visit https://neurostars.org/search?q=NO_VALID_DATA_FOUND_FOR_SUBJECT 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 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.
Any help would be appreciated.
With regards
-Korann