Bids-validator errors

1

Dear all,

I really appreciate your help.
I used https://1526-37161308-gh.circle-artifacts.com/0/root/web_version/index.html
(https://bids-standard.github.io/bids-validator/ gave additional errors…)

Nifti_errors (5).txt (32.3 KB)

57
Screen Shot 2019-09-17 at 16.27.57.png1080×385 42.3 KB

  1. File Path: 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.
    True. How can it ignore missing files?
  2. File Path: Not all subjects/sessions/runs have the same scanning parameters.
    Its true, but this is my data.
  3. File Path: Tabular file does not have accompanying data dictionary.
    What does it mean!?
    I added “response” Columns (hedonic ratings) to the _events.tsv files (subjects ratings of hedonic). using github.io/bids-validator there was an error:(for all subjects)
    Columns: response not defined, please define in: /sub-02/func/sub-02_events.json, /sub-02/func/sub-02_task-odors_events.json,/sub-02/sub-02_events.json,/sub-02/sub-02_task-odors_events.json,/events.json,/task-odors_events.json,/sub-02/func/sub-02_task-odors_run-02_events.json

Thank you!!!

2

Hi @Tali_Weiss,

Just a note that these are warnings, not errors, so if you’re comfortable with them, they can be safely ignored.

  1. This is just your knowledge. There isn’t a standardized way to indicate that a file is expected to be missing.
  2. Also just an advisory one. If your data is meant to be heterogeneous, then carry on.
  3. This is a best practices note. See https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#tabular-files for how to add metadata to a tabular file.

Best,
Chris

3

Thank you Chris, I’m almost there :slight_smile: (only warnings, no errors)

  1. I have a few notes i like to add regarding subjects’ performance during the scan (“for example: fell asleep during X trials”, the number of dicoms I recommend to skip and trim…)
    Where can i add those notes? a pdf/txt file in a derivatives folder?
    Furthermore, i like to add LabChart data (raw recording of stimuli onset, TRs, response…) should I add those to the derivatives folder as well?

  2. about the warning: Tabular file does not have accompanying data dictionary
    I created one file task-NAME_events.json that apply to all events.
    Why I still get this Warning?

  3. Finally, after using HeuDiConv, run pydeface on T1W so get sub-01_T1w_defaced.nii.gz
    Next, I rename sub-01_T1w_defaced.nii.gz > ub-01_T1w.nii.gz;
    Is there a better way?

thank you again,
Tali

4

You can add anything you like to a README file. That seems an appropriate place to me. If there are more systematic, per-subject notes that make sense to save as tabular data, consider the phenotype/ directory.

If it’s data that is covered by the spec, then the thing to do is to format the data as indicated in the spec. The original data can be placed in sourcedata/. sourcedata/ is not inspected by the validator, but it’s recommended to follow a mirrored structure, so that the correspondence between raw data and BIDS-prepared data is clear.

If it is data that is not covered by the spec, the recommendation is to follow BIDS as closely as you can, while placing it in your normal BIDS directory (or sourcedata/, as it seems appropriate). This, however, will cause the validator to fail, so you will need to list these non-conformant files in a .bidsignore text file at the root of your dataset.

We’re working on some clarifying language right now, but the current draft is:

Unspecified data

Additional files and folders containing raw data MAY be added as needed for special cases. All non-standard file entities SHOULD conform to BIDS-style naming conventions, including alphabetic entities and suffixes and alphanumeric labels/indices. Non-standard suffixes SHOULD reflect the nature of the data, and existing entities SHOULD be used when appropriate. For example, an ASSET calibration scan might be named sub-01_acq-ASSET_calibration.nii.gz .

Non-standard files and directories should be named with care. Future BIDS efforts may standardize new entities and suffixes, changing the meaning of file names and setting requirements on their contents or metadata. Validation and parsing tools MAY treat the presence of non-standard files and directories as an error, so consult the details of these tools for mechanisms to suppress warnings or provide interpretations of your file names.

Could you share the full text of the warning? It may apply to other TSV files, there could be missing columns, or there could be a bug in the validator.

This seems perfectly reasonable to me.

5

thank you for all your help!

taliweiss_errors.txt (24.9 KB)
sub-05_scans.txt (366 Bytes)
sub-05_task-odors_run-02_events.txt (456 Bytes)
task-odors_events.txt (649 Bytes)

6

Are these files named *.tsv in your directory, or *.txt?

7

.tsv (“select images or files from your device (jpg, jpeg, png, gif, txt)”)

8

I may be missing something, but this looks fine to me.

9

There might be a bug in the validator regarding this. While testing I couldn’t get the validator to not issue the warning with a json file for participants.tsv: