Indexing is hardcoded #72

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1. kaitj commented on Apr 30, 2026

   

   kaitj

   on Apr 30, 2026

   Last edited by kaitj

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   I am having a little bit of trouble my head around this one (more how much of this should be handled by validation vs indexing), though I do agree, generally, that if possible we should follow the schema.

   Currently:

   • b2t only indexes if a directory follows the subject/session directory structure (e.g. it doesn't index the Freesurfer output directories as they are outputted) and the identified files pass validation
   • b2t doesn't make a distinction between "raw" and "derivative" datasets, just that if its a "bids" dataset. Unless I am missing something, I think this is still fine even with the schema

   Initial thoughts:

   • The schema entities that immediately relevant to b2t (and these might not span across all levels) are:

     subject:
      entity: subject
      level: optional
      opaque: false
      subdirs:
        - session
        - datatype
     session:
      entity: session
      level: optional
      opaque: false
      subdirs:
        - datatype
     template:
      entity: template
      level: optional
      opaque: false
      subdirs:
        - cohort
        - datatype
     datatype:
      value: datatype
      level: optional
      opaque: false

   • we probably also want to consider all the directories where the entity is opaque: false with some exceptions (e.g. recursively searching through the derivatives directory)

   Just some brief thoughts, but agree we should investigate this further.