mrsiprep.io.bids

Input layout discovery for MRSIPrep.

Functions

load_bids_filters(path)

Parse a --bids-filter-file JSON document.

Classes

BIDSLayout(bids_dir[, filters])

Minimal path resolver for the MRSI-Metabolic-Connectome derivative layout.

Recording(subject, session)

class mrsiprep.io.bids.BIDSLayout(bids_dir, filters=None)[source]

Bases: object

Minimal path resolver for the MRSI-Metabolic-Connectome derivative layout.

Parameters:

  • bids_dir (str | Path)

  • filters (dict | None)

brain_mask(subject, session)[source]
Parameters:

  • subject (str)

  • session (str | None)

Return type:

Path | None

cat12_probseg(subject, session, index)[source]
Parameters:

  • subject (str)

  • session (str | None)

  • index (int)

Return type:

Path | None

chimera_atlas(subject, session, scheme, scale, grow=2, space='orig')[source]
Parameters:

  • subject (str)

  • session (str | None)

  • scheme (str)

  • scale (int)

  • grow (int)

  • space (str)

Return type:

Path | None

discover_recordings()[source]
Return type:

list[Recording]

mrsi_map(subject, session, desc, met=None, option=None, space='orig', res=None, construct=False)[source]
Parameters:

  • subject (str)

  • session (str | None)

  • desc (str)

  • met (str | None)

  • option (str | None)

  • space (str)

  • res (str | int | None)

  • construct (bool)

Return type:

Path | None

raw_t1(subject, session, reference_name=None)[source]
Parameters:

  • subject (str)

  • session (str | None)

  • reference_name (str | None)

Return type:

Path | None

t1(subject, session, pattern='desc-brain_T1w')[source]
Parameters:

  • subject (str)

  • session (str | None)

  • pattern (str)

Return type:

Path | None

transform(subject, session, stage, direction='forward')[source]
Parameters:

  • subject (str)

  • session (str | None)

  • stage (str)

  • direction (str)

Return type:

list[Path]

class mrsiprep.io.bids.Recording(subject: 'str', session: 'str | None')[source]

Bases: object

Parameters:

  • subject (str)

  • session (str | None)

property prefix: str
session: str | None
subject: str
mrsiprep.io.bids.load_bids_filters(path)[source]

Parse a --bids-filter-file JSON document.

Only the "t1w" top-level key is currently supported (the one input MRSIPrep has ambiguous-candidate logic for today, in BIDSLayout.raw_t1()). Any other top-level key raises immediately rather than being silently ignored, since a user copying an fMRIPrep-style filter file (with "bold"/"fmap"/etc keys) should get fast feedback that those aren't supported here yet.

Parameters:

path (str | Path | None)

Return type:

dict