update parse_filename evaluated string set (anat, func, dwi)

[fishpm]

Updated set of evaluated strings via parse_filename for anat, func, and dwi according to BIDS v1.9.0. Other modalities might also need to be updated. Probably a more clever way to encode evaluated string more dynamically?

[gllmflndn]

Thanks @fishpm! I presume it supersedes your previous PR?

It looks good to me and it seems to also cover @CPernet's other PR.

If @Remi-Gau and @CPernet are OK with it, I'm happy to merge this.

Concerning your last question, the future is to use https://github.com/bids-standard/bids-matlab/.

[Remi-Gau]

Need to check in detail (can't right now because at a conference) but wait before merging because I think some entities have been added in the wrong place.

[fishpm]

Thanks for the quick look. I was looking at the bids documentation (v1.9.0) when adding entities, but would not rule out making an error.

[Remi-Gau]

a few things to fix that are easy to miss: may usually requires digging into the schema or the appendix or the starter kit to be sure

[Remi-Gau]

no task in diffusion according to the yml schema:

https://github.com/bids-standard/bids-specification/blob/c7cabedc0870acc454fdc01af223379f797a011f/src/schema/rules/files/raw/dwi.yaml#L14

[Remi-Gau]

no part, chunk or echo for physio (also note that this assumes that this physio is for func data)

I have set up the starter kit to give you all the BIDS filename templates:

https://bids-standard.github.io/bids-starter-kit/folders_and_files/files.html#func-functional-mri

[Remi-Gau]

no part, chunk, echo or recording for events files (also note that this assumes that this is for func data)

https://bids-standard.github.io/bids-starter-kit/folders_and_files/files.html#func-functional-mri

[Remi-Gau]

This is missing the entities from quantitative MRI:

• mt
• inv
• flip

https://bids-standard.github.io/bids-starter-kit/folders_and_files/files.html#anat-anatomical-mri

https://bids-specification.readthedocs.io/en/latest/appendices/qmri.html#inputs-are-file-collections

[CPernet]

it would be more work but better to parse BIDS yaml files to search/filter files - how do we do it bids-matlab? -- There is a parser here

[Remi-Gau]

bids-matlab has a class to help navigate the json version of the schema that bids-matlab gets shipped with:

https://bids-matlab.readthedocs.io/en/main/schema.html

The names of the methods are bit on the verbose side and the API could probably be improved but easier than browsing the yml files in general.

schema = bids.Schema
suffix_groups = schema.list_suffix_groups('func')
suffix_group_of_interest = suffix_groups.func
entities = schema.return_entities_for_suffix_group(suffix_group_of_interest)

schema = 
  Schema with properties:

                 content: [1×1 struct]
                 verbose: 0
          is_bids_schema: 0
    load_schema_metadata: 0

suffix_groups = 
  struct with fields:

                func: [1×1 struct]
               phase: [1×1 struct]
         events__mri: [1×1 struct]
    timeseries__func: [1×1 struct]

suffix_group_of_interest = 
  struct with fields:

      suffixes: {3×1 cell}
    extensions: {3×1 cell}
     datatypes: {'func'}
      entities: [1×1 struct]

entities =
  1×11 cell array
  Columns 1 through 9
    {'sub'}    {'ses'}    {'task'}    {'acq'}    {'ce'}    {'rec'}    {'dir'}    {'run'}    {'echo'}
  Columns 10 through 11
    {'part'}    {'chunk'}

[CPernet]

also now I PR @fishpm to fix PET data (task not mandatory, parse trc, do not parse acq)