Terminology differences between BIDS-schema and the query "API"

[Remi-Gau]

I think that are differences between the code and the schema we might want to "clarify" or realign before moving on.

BIDS-schema

Modalities contain datatypes.

mri modality contains :

• "anat"
• "dwi"
• "fmap"
• "func"
• "perf"

See the whole listing here:

{
  "mri": {
    "name": "Magnetic Resonance Imaging",
    "datatypes": [
      "anat",
      "dwi",
      "fmap",
      "func",
      "perf"
    ]
  },
  "eeg": {
    "name": "Electroencephalography",
    "datatypes": [
      "eeg"
    ]
  },
  "ieeg": {
    "name": "Intracranial Electroencephalography",
    "datatypes": [
      "ieeg"
    ]
  },
  "meg": {
    "name": "Magnetoencephalography",
    "datatypes": [
      "meg"
    ]
  },
  "beh": {
    "name": "Behavioral experiments",
    "datatypes": [
      "beh"
    ]
  }

Dataypes contain several "groups" with several possible suffixes for each group.

An example of one of those "groups" for that anat datatype.

  {
    "suffixes": [
      "T1w",
      "T2w",
      "PDw",
      "T2starw",
      "FLAIR",
      "inplaneT1",
      "inplaneT2",
      "PDT2",
      "angio"
    ],
    "extensions": [
      ".nii.gz",
      ".nii",
      ".json"
    ],
    "entities": {
      "sub": "required",
      "ses": "optional",
      "run": "optional",
      "acq": "optional",
      "ce": "optional",
      "rec": "optional",
      "part": "optional"
    }
  },

BIDS-matlab code

Especially bids.query has a slightly different meaning for some of those words.

Modality will mean one of the following:

• anat
• func
• fmap
• beh
• dwi
• eeg
• meg
• ieeg
• pet

There is no datatype in the code but we a type that usually refers to the suffix of a given file (bold, T1w...).

I am tempted to realign our terminology on the schema and that of the BIDS specs.

It should not be too complicated to do but it would change how the calls to bids.query.

PS: will put that on the agenda of the next meeting.