mrsiprep.workflows.mrsi

MRSI preprocessing workflow.

Functions

run_mrsi_workflow(config, subject, session, ...)

Preprocess one recording's native-space MRSI maps.

Classes

MRSIResult(raw_maps, preproc_maps, ...[, ...])

Native-space MRSI derivatives produced by run_mrsi_workflow().
class mrsiprep.workflows.mrsi.MRSIResult(raw_maps, preproc_maps, corrected_maps, crlb_maps, snr_map, linewidth_map, water_map, brainmask, reference, qcmasks, qc_summary, t1_correction_provenance=None)[source]

Bases: object

Native-space MRSI derivatives produced by run_mrsi_workflow().

All paths are in MRSI-native space; per-metabolite maps are keyed by metabolite name (e.g. "CrPCr", matching --metabolites/--ref-met).

Variables:

  • raw_maps -- Metabolite signal maps as copied into the derivatives tree, unmodified from derivatives/mrsi-orig/.

  • preproc_maps -- Metabolite maps after spike detection and biharmonic repair (see mrsiprep.mrsi.filtering.filter_metabolite_maps()).

  • corrected_maps -- Identical to preproc_maps unless config.t1_correction == "literature", in which case this holds the T1-saturation-corrected maps (see mrsiprep.mrsi.t1_correction.apply_t1_correction()). Partial volume correction happens later (see mrsiprep.mrsi.pvc.run_pvc()), not in this workflow, and always consumes corrected_maps as its input.

  • t1_correction_provenance -- Per-metabolite T1-correction summary rows (TR, flip angle, T1, factor, source, warnings), or None when config.t1_correction == "none".

  • crlb_maps -- Per-metabolite Cramér-Rao lower bound maps, copied through unchanged from the raw inputs.

  • snr_map -- Whole-brain signal-to-noise-ratio map, if the input BIDS layout provided one.

  • linewidth_map -- Whole-brain linewidth/FWHM map, if provided.

  • water_map -- Water-reference image, if provided (used for coil combination / normalization upstream of mrsiprep, not recomputed here).

  • brainmask -- MRSI-native brainmask, either taken from the inputs or derived when missing (see mrsiprep.mrsi.masks.ensure_brainmask()).

  • reference -- The reference-metabolite image used to drive MRSI→T1w registration (config.ref_met, default CrPCr).

  • qcmasks -- Per-metabolite voxel-quality masks (SNR/CRLB/FWHM thresholds applied), keyed the same way as preproc_maps.

  • qc_summary -- Path to the per-recording QC summary table produced alongside qcmasks.

Parameters:

  • raw_maps (dict[str, Path])

  • preproc_maps (dict[str, Path])

  • corrected_maps (dict[str, Path])

  • crlb_maps (dict[str, Path])

  • snr_map (Path | None)

  • linewidth_map (Path | None)

  • water_map (Path | None)

  • brainmask (Path)

  • reference (Path)

  • qcmasks (dict[str, Path])

  • qc_summary (Path)

  • t1_correction_provenance (list[dict] | None)

brainmask: Path
corrected_maps: dict[str, Path]
crlb_maps: dict[str, Path]
linewidth_map: Path | None
preproc_maps: dict[str, Path]
qc_summary: Path
qcmasks: dict[str, Path]
raw_maps: dict[str, Path]
reference: Path
snr_map: Path | None
t1_correction_provenance: list[dict] | None = None
water_map: Path | None
mrsiprep.workflows.mrsi.run_mrsi_workflow(config, subject, session, inputs)[source]

Preprocess one recording's native-space MRSI maps.

Copies raw inputs into the derivatives tree, ensures a brainmask exists (deriving one from the water/metabolite maps if the input layout didn't provide one), filters metabolite maps (spike detection and biharmonic repair), builds the reference-metabolite image used to drive registration, and computes voxel-level quality masks from the SNR/CRLB/FWHM thresholds in config.

Parameters:

  • config -- Run-wide mrsiprep.config.settings.MRSIPrepConfig.

  • subject (str) -- BIDS subject label, without the sub- prefix.

  • session (str | None) -- BIDS session label without the ses- prefix, or None for session-less datasets.

  • inputs (MRSIInputs) -- The recording's raw MRSI inputs as discovered by mrsiprep.io.loaders.load_mrsi_inputs() (metabolite/CRLB maps, SNR/linewidth/water maps, brainmask -- any of which may be None except metabolite_maps).

Returns:

MRSIResult with all derivatives written to config.derivative_dir and referenced by path.

Return type:

MRSIResult