mrsiprep.config.settings

Runtime configuration objects.

Classes

MRSIPrepConfig(bids_dir, output_dir, ...)

class mrsiprep.config.settings.MRSIPrepConfig(bids_dir: 'Path', output_dir: 'Path', analysis_level: 'str', participant_label: 'list[str]' = <factory>, session_label: 'list[str]' = <factory>, participants_file: 'Path | None' = None, bids_filter_file: 'Path | None' = None, metabolites: 'list[str] | None' = None, quality_metrics: 'list[str]' = <factory>, snr_min: 'float' = 4.0, linewidth_max: 'float' = 0.1, crlb_max: 'float' = 20.0, processing_mode: 'str' = 'mni-norm', tissue_backend: 'str' = 'synthseg-fast', registration_backend: 'str' = 'ants', ants_mrsi_to_t1_transform: 'str' = 'sr', ants_t1_to_mni_transform: 'str' = 's', fsl_mrsi_to_t1_dof: 'int' = 6, fsl_mrsi_to_t1_init: 'str' = 'flirt', fsl_t1_to_mni_dof: 'int' = 12, fsl_cost: 'str' = 'corratio', fsl_deformable: 'bool' = True, fsl_fnirt_warpres: 'tuple[int, int, int] | None'=None, fsl_fnirt_lambda: 'str' = '300, 200, 150, 150', normalization: 'str' = 'simple', output_spaces: 'list[str]' = <factory>, output_mrsi_t1w: 'bool' = False, mni_resolution: 'str' = 'origres', registration_t1_target: 'str | None' = None, csf_pv_threshold: 'float' = 0.95, parcellation_mode: 'str | None' = None, synthseg_mode: 'str' = 'robust', chimera_scheme: 'str' = 'LFMIHIFIS', chimera_scale: 'int' = 3, chimera_grow: 'int' = 2, atlas: 'str' = 'chimera-LFMIHIFIS-3', custom_atlas: 'Path | None' = None, custom_atlas_lut: 'Path | None' = None, fs_subjects_dir: 'Path | None' = None, write_connectivity: 'bool' = False, connectivity_method: 'str' = 'spearman', connectivity_space: 'str' = 'MRSI', connectivity_n_perturbations: 'int' = 50, connectivity_sigma_scale: 'float' = 2.0, connectivity_exclude_parcels: 'str | None' = None, connectivity_max_parcel_id: 'int | None' = None, regional_summary: 'str' = 'mean', nthreads: 'int' = 16, nproc: 'int' = 1, ref_met: 'str | None' = None, t1_pattern: 'str' = 'desc-brain_T1w', transform: 'str' = '', filter_biharmonic: 'bool' = True, filter_fwhm_mm: 'float | None' = None, spike_percentile: 'float' = 99.0, spike_max_cluster_voxels: 'int | None' = None, no_pvc: 'bool' = False, t1_correction: 'str' = 'none', t1_correction_water_status: 'str' = 'unknown', overwrite_t1corr: 'bool' = False, longitudinal: 'bool' = False, transform_spikemask: 'bool' = False, overwrite: 'bool' = False, overwrite_filt: 'bool' = False, overwrite_seg: 'bool' = False, overwrite_pve: 'bool' = False, overwrite_t1_reg: 'bool' = False, overwrite_mni_reg: 'bool' = False, overwrite_transform: 'bool' = False, overwrite_chimera: 'bool' = False, work_dir: 'Path | None' = None, verbose: 'int' = 1, validate_only: 'bool' = False, skip_file_integrity_check: 'bool' = False, check_external_libs: 'bool' = False, stop_on_first_crash: 'bool' = False, preset_citation: 'dict | None' = None)

Bases: object

Parameters:

• bids_dir (Path)

• output_dir (Path)

• analysis_level (str)

• participant_label (list[str])

• session_label (list[str])

• participants_file (Path | None)

• bids_filter_file (Path | None)

• metabolites (list[str] | None)

• quality_metrics (list[str])

• snr_min (float)

• linewidth_max (float)

• crlb_max (float)

• processing_mode (str)

• tissue_backend (str)

• registration_backend (str)

• ants_mrsi_to_t1_transform (str)

• ants_t1_to_mni_transform (str)

• fsl_mrsi_to_t1_dof (int)

• fsl_mrsi_to_t1_init (str)

• fsl_t1_to_mni_dof (int)

• fsl_cost (str)

• fsl_deformable (bool)

• fsl_fnirt_warpres (tuple[int, int, int] | None)

• fsl_fnirt_lambda (str)

• normalization (str)

• output_spaces (list[str])

• output_mrsi_t1w (bool)

• mni_resolution (str)

• registration_t1_target (str | None)

• csf_pv_threshold (float)

• parcellation_mode (str | None)

• synthseg_mode (str)

• chimera_scheme (str)

• chimera_scale (int)

• chimera_grow (int)

• atlas (str)

• custom_atlas (Path | None)

• custom_atlas_lut (Path | None)

• fs_subjects_dir (Path | None)

• write_connectivity (bool)

• connectivity_method (str)

• connectivity_space (str)

• connectivity_n_perturbations (int)

• connectivity_sigma_scale (float)

• connectivity_exclude_parcels (str | None)

• connectivity_max_parcel_id (int | None)

• regional_summary (str)

• nthreads (int)

• nproc (int)

• ref_met (str | None)

• t1_pattern (str)

• transform (str)

• filter_biharmonic (bool)

• filter_fwhm_mm (float | None)

• spike_percentile (float)

• spike_max_cluster_voxels (int | None)

• no_pvc (bool)

• t1_correction (str)

• t1_correction_water_status (str)

• overwrite_t1corr (bool)

• longitudinal (bool)

• transform_spikemask (bool)

• overwrite (bool)

• overwrite_filt (bool)

• overwrite_seg (bool)

• overwrite_pve (bool)

• overwrite_t1_reg (bool)

• overwrite_mni_reg (bool)

• overwrite_transform (bool)

• overwrite_chimera (bool)

• work_dir (Path | None)

• verbose (int)

• validate_only (bool)

• skip_file_integrity_check (bool)

• check_external_libs (bool)

• stop_on_first_crash (bool)

• preset_citation (dict | None)

analysis_level: str

ants_mrsi_to_t1_transform: str = 'sr'

ants_t1_to_mni_transform: str = 's'

atlas: str = 'chimera-LFMIHIFIS-3'

bids_dir: Path

bids_filter_file: Path | None = None

check_external_libs: bool = False

chimera_grow: int = 2

chimera_scale: int = 3

chimera_scheme: str = 'LFMIHIFIS'

connectivity_exclude_parcels: str | None = None

connectivity_max_parcel_id: int | None = None

connectivity_method: str = 'spearman'

connectivity_n_perturbations: int = 50

connectivity_sigma_scale: float = 2.0

connectivity_space: str = 'MRSI'

crlb_max: float = 20.0

csf_pv_threshold: float = 0.95

custom_atlas: Path | None = None

custom_atlas_lut: Path | None = None

property derivative_dir: Path

filter_biharmonic: bool = True

filter_fwhm_mm: float | None = None

property freesurfer_dir: Path

fs_subjects_dir: Path | None = None

fsl_cost: str = 'corratio'

fsl_deformable: bool = True

fsl_fnirt_lambda: str = '300,200,150,150'

fsl_fnirt_warpres: tuple[int, int, int] | None = None

fsl_mrsi_to_t1_dof: int = 6

fsl_mrsi_to_t1_init: str = 'flirt'

fsl_t1_to_mni_dof: int = 12

linewidth_max: float = 0.1

property logs_dir: Path

longitudinal: bool = False

metabolites: list[str] | None = None

mni_resolution: str = 'origres'

no_pvc: bool = False

normalization: str = 'simple'

nproc: int = 1

nthreads: int = 16

output_dir: Path

output_mrsi_t1w: bool = False

output_spaces: list[str]

overwrite: bool = False

overwrite_chimera: bool = False

overwrite_filt: bool = False

overwrite_mni_reg: bool = False

overwrite_pve: bool = False

overwrite_seg: bool = False

overwrite_t1_reg: bool = False

overwrite_t1corr: bool = False

overwrite_transform: bool = False

parcellation_mode: str | None = None

participant_label: list[str]

participants_file: Path | None = None

preset_citation: dict | None = None

processing_mode: str = 'mni-norm'

quality_metrics: list[str]

ref_met: str | None = None

regional_summary: str = 'mean'

registration_backend: str = 'ants'

registration_t1_target: str | None = None

resolve_cpu_budget()

Coerce nproc*nthreads to the available CPU count.

Returns (nproc, nthreads, warning) where warning is set (and nthreads reduced) if the requested total thread budget exceeds the machine's CPU count.

Return type:

tuple[int, int, str | None]

session_label: list[str]

skip_file_integrity_check: bool = False

snr_min: float = 4.0

spike_max_cluster_voxels: int | None = None

spike_percentile: float = 99.0

stop_on_first_crash: bool = False

synthseg_mode: str = 'robust'

t1_correction: str = 'none'

t1_correction_water_status: str = 'unknown'

t1_pattern: str = 'desc-brain_T1w'

tissue_backend: str = 'synthseg-fast'

to_dict()

Return type:

dict

transform: str = ''

transform_spikemask: bool = False

validate_only: bool = False

verbose: int = 1

work_dir: Path | None = None

write_connectivity: bool = False