bids-validator

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• closes #1755

~~Participants was being defined as a const and assigned null. Usual use case for consts is to give it an actual array or object with reference and then later on push to that array or object. For whatever reason tsv validation attempts to reassign the participants reference it gets.~~

Aug 08 '23 14:08 rwblair

Codecov Report

Patch coverage: 100.00% and project coverage change: -2.32% :warning:

Comparison is base (5ec0b3d) 85.71% compared to head (8122bcb) 83.40%.

:exclamation: Current head 8122bcb differs from pull request most recent head cf46045. Consider uploading reports for the commit cf46045 to get more accurate results

@@            Coverage Diff             @@
##           master    #1772      +/-   ##
==========================================
- Coverage   85.71%   83.40%   -2.32%     
==========================================
  Files         130       92      -38     
  Lines        6575     3893    -2682     
  Branches     1524     1270     -254     
==========================================
- Hits         5636     3247    -2389     
+ Misses        833      548     -285     
+ Partials      106       98       -8     

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Aug 08 '23 14:08 codecov[bot]

We now get code 67 NO_VALID_DATA_FOUND_FOR_SUBJECT for any bids-examples with a participants.tsv.

ieeg_motorMiller2007 has rows in participants.tsv that have no directories in the dataset. Throws code 49 PARTICIPANT_ID_MISMATCH

Aug 08 '23 15:08 rwblair

ieeg_motorMiller2007 has rows in participants.tsv that have no directories in the dataset. Throws code 49 PARTICIPANT_ID_MISMATCH

@dorahermes could you look into this, please?

Aug 09 '23 07:08 sappelhoff

Suggestion from maintainers meeting: for legacy validator automatically add 67 to ignored codes if --ignore-nifti-headers used, prevent us from having to edit ignored codes in bids-examples tests.

Aug 10 '23 17:08 rwblair

It seems that 3 subjects are missing folders (jf, gf, jp). Data from these subjects is located in the original ECoG library. Let me know if you prefer option 1 or 2:

1. Remove these three subjects from the BIDS example participants.tsv file
2. I could convert these 3 subjects to BIDS and do a pull request to update accordingly

(I am not sure why I missed these subjects in the conversion. One thing I vaguely remember is that there was a mismatch in electrodes and channels, but the current version of the ECoG library does not have any mismatches. There was an update in 2022 though.)

Aug 10 '23 18:08 dorahermes

IMO if the usefulness of the dataset as an example isn't damaged by dropping the subjects, removing them from participants.tsv seems sensible to me.

Aug 10 '23 18:08 effigies

IMO if the usefulness of the dataset as an example isn't damaged by dropping the subjects, removing them from participants.tsv seems sensible to me.

agreed

Aug 14 '23 09:08 sappelhoff