Index

A

all_exist() (in module mrsiprep.registration.transforms) analysis_level (mrsiprep.config.settings.MRSIPrepConfig attribute) anat_derivative() (in module mrsiprep.io.naming) AnatomicalResult (class in mrsiprep.workflows.anatomical) ants_mrsi_to_t1_transform (mrsiprep.config.settings.MRSIPrepConfig attribute) ants_t1_to_mni_transform (mrsiprep.config.settings.MRSIPrepConfig attribute)

ants_transform_prefix() (in module mrsiprep.registration.transforms) ANTsError apply_image_transform() (in module mrsiprep.registration.transforms) apply_transforms() (in module mrsiprep.interfaces.ants) (in module mrsiprep.interfaces.fsl) apply_transforms_cli() (in module mrsiprep.interfaces.ants) atlas (mrsiprep.config.settings.MRSIPrepConfig attribute)

B

beta_gm (mrsiprep.parcellation.tissue_regression.RegressionResult attribute) beta_wm (mrsiprep.parcellation.tissue_regression.RegressionResult attribute) bias (mrsiprep.parcellation.tissue_regression.RegressionResult attribute) bids_dir (mrsiprep.config.settings.MRSIPrepConfig attribute) bids_filter_file (mrsiprep.config.settings.MRSIPrepConfig attribute) BIDSLayout (class in mrsiprep.io.bids)

biharmonic_repair() (in module mrsiprep.mrsi.filtering) brain_mask (mrsiprep.workflows.anatomical.AnatomicalResult attribute) brain_mask() (mrsiprep.io.bids.BIDSLayout method) brainmask (mrsiprep.io.loaders.MRSIInputs attribute) (mrsiprep.workflows.mrsi.MRSIResult attribute) build_parcel_indexer() (in module mrsiprep.connectivity.connectivity) build_subject_template() (in module mrsiprep.registration.subject_template)

C

cat12_probseg() (mrsiprep.io.bids.BIDSLayout method) check_chimera() (in module mrsiprep.interfaces.chimera) check_external_libs (mrsiprep.config.settings.MRSIPrepConfig attribute) check_license() (in module mrsiprep.interfaces.freesurfer) chimera_atlas() (mrsiprep.io.bids.BIDSLayout method) chimera_derivative() (in module mrsiprep.io.naming) chimera_grow (mrsiprep.config.settings.MRSIPrepConfig attribute) chimera_scale (mrsiprep.config.settings.MRSIPrepConfig attribute) chimera_scheme (mrsiprep.config.settings.MRSIPrepConfig attribute) ChimeraError collect_recordings() (in module mrsiprep.workflows.participant) compose_longitudinal_t1_to_mni() (in module mrsiprep.registration.t1_to_mni) compute_metabolic_profiles() (in module mrsiprep.connectivity.connectivity) compute_metabolite_connectivity() (in module mrsiprep.connectivity.connectivity) condition_number (mrsiprep.parcellation.tissue_regression.RegressionResult attribute) connectivity_exclude_parcels (mrsiprep.config.settings.MRSIPrepConfig attribute) connectivity_max_parcel_id (mrsiprep.config.settings.MRSIPrepConfig attribute) connectivity_method (mrsiprep.config.settings.MRSIPrepConfig attribute) connectivity_n_perturbations (mrsiprep.config.settings.MRSIPrepConfig attribute)

connectivity_sigma_scale (mrsiprep.config.settings.MRSIPrepConfig attribute) connectivity_space (mrsiprep.config.settings.MRSIPrepConfig attribute) ConnectivityResult (class in mrsiprep.connectivity.connectivity) convolve_with_psf() (in module mrsiprep.tissue.psf) convolve_with_psf_separable() (in module mrsiprep.tissue.psf) copy_tissue_to_derivatives() (in module mrsiprep.tissue.fractions) corrected_maps (mrsiprep.workflows.mrsi.MRSIResult attribute) correlate_metabolic_profiles() (in module mrsiprep.connectivity.connectivity) coverage_figure_derivative() (in module mrsiprep.io.naming) coverage_report_dir() (in module mrsiprep.io.naming) coverage_report_html() (in module mrsiprep.io.naming) create_brain_csf_t1() (in module mrsiprep.workflows.anatomical) create_tissue_4d() (in module mrsiprep.mrsi.pvc) crlb_maps (mrsiprep.io.loaders.MRSIInputs attribute) (mrsiprep.workflows.mrsi.MRSIResult attribute) crlb_max (mrsiprep.config.settings.MRSIPrepConfig attribute) csf_pv_threshold (mrsiprep.config.settings.MRSIPrepConfig attribute) custom_atlas (mrsiprep.config.settings.MRSIPrepConfig attribute) custom_atlas_lut (mrsiprep.config.settings.MRSIPrepConfig attribute)

D

default_fnirt_warpres() (in module mrsiprep.interfaces.fsl) default_spike_max_cluster_voxels() (in module mrsiprep.mrsi.filtering)

derivative_dir (mrsiprep.config.settings.MRSIPrepConfig property) discover_recordings() (mrsiprep.io.bids.BIDSLayout method)

E

ensure_brainmask() (in module mrsiprep.mrsi.masks) ensure_work_dirs() (in module mrsiprep.workflows.base) error (mrsiprep.workflows.participant.RecordingStatus attribute)

export_connectivity() (in module mrsiprep.connectivity.export) export_metabolic_profiles() (in module mrsiprep.connectivity.export) extract_regional_metabolites() (in module mrsiprep.parcellation.extraction) extract_t1_synthseg() (in module mrsiprep.tissue.synthseg_fast)

F

features (mrsiprep.connectivity.connectivity.MetabolicProfileResult attribute) filter_biharmonic (mrsiprep.config.settings.MRSIPrepConfig attribute) filter_fwhm_mm (mrsiprep.config.settings.MRSIPrepConfig attribute) filter_metabolite_maps() (in module mrsiprep.mrsi.filtering) find_freesurfer_tool() (in module mrsiprep.tissue.synthseg_fast) fit_tissue_regression() (in module mrsiprep.parcellation.tissue_regression) forward (mrsiprep.registration.mrsi_to_t1.MRSIToT1Result attribute) (mrsiprep.registration.t1_to_mni.T1ToMNIResult attribute) freesurfer_dir (mrsiprep.config.settings.MRSIPrepConfig property) freesurfer_subject_id() (in module mrsiprep.interfaces.freesurfer)

FreeSurferError fs_subjects_dir (mrsiprep.config.settings.MRSIPrepConfig attribute) fsl_cost (mrsiprep.config.settings.MRSIPrepConfig attribute) fsl_deformable (mrsiprep.config.settings.MRSIPrepConfig attribute) fsl_fnirt_lambda (mrsiprep.config.settings.MRSIPrepConfig attribute) fsl_fnirt_warpres (mrsiprep.config.settings.MRSIPrepConfig attribute) fsl_mrsi_to_t1_dof (mrsiprep.config.settings.MRSIPrepConfig attribute) fsl_mrsi_to_t1_init (mrsiprep.config.settings.MRSIPrepConfig attribute) fsl_t1_to_mni_dof (mrsiprep.config.settings.MRSIPrepConfig attribute) FSLError fuzzy_cmeans_segment() (in module mrsiprep.tissue.fuzzy_cmeans)

G

generate_reference() (in module mrsiprep.mrsi.reference) get_spike_mask() (in module mrsiprep.mrsi.filtering)

gm_weighted (mrsiprep.connectivity.connectivity.ConnectivityResult attribute) (mrsiprep.connectivity.connectivity.MetabolicProfileResult attribute)

H

hamming_sinc_psf_kernel() (in module mrsiprep.tissue.psf)

I

init_derivative() (in module mrsiprep.io.derivatives)

inverse (mrsiprep.registration.mrsi_to_t1.MRSIToT1Result attribute) (mrsiprep.registration.t1_to_mni.T1ToMNIResult attribute)

L

linewidth_map (mrsiprep.io.loaders.MRSIInputs attribute) (mrsiprep.workflows.mrsi.MRSIResult attribute) linewidth_max (mrsiprep.config.settings.MRSIPrepConfig attribute) load_bids_filters() (in module mrsiprep.io.bids)

load_existing_cat12() (in module mrsiprep.tissue.fractions) load_mrsi_inputs() (in module mrsiprep.io.loaders) load_mrsinmrs() (in module mrsiprep.io.mrsinmrs) logs_dir (mrsiprep.config.settings.MRSIPrepConfig property) longitudinal (mrsiprep.config.settings.MRSIPrepConfig attribute)

M

make_quality_masks() (in module mrsiprep.mrsi.quality) MetabolicProfileResult (class in mrsiprep.connectivity.connectivity) metabolite_maps (mrsiprep.io.loaders.MRSIInputs attribute) metabolites (mrsiprep.config.settings.MRSIPrepConfig attribute) (mrsiprep.connectivity.connectivity.ConnectivityResult attribute) (mrsiprep.connectivity.connectivity.MetabolicProfileResult attribute) method (mrsiprep.connectivity.connectivity.ConnectivityResult attribute) mni_resolution (mrsiprep.config.settings.MRSIPrepConfig attribute) module mrsiprep.config.defaults mrsiprep.config.settings mrsiprep.connectivity.connectivity mrsiprep.connectivity.export mrsiprep.interfaces.ants mrsiprep.interfaces.chimera mrsiprep.interfaces.freesurfer mrsiprep.interfaces.fsl mrsiprep.io.bids mrsiprep.io.derivatives mrsiprep.io.loaders mrsiprep.io.mrsinmrs mrsiprep.io.naming mrsiprep.io.validators mrsiprep.mrsi.filtering mrsiprep.mrsi.masks mrsiprep.mrsi.pvc mrsiprep.mrsi.quality mrsiprep.mrsi.reference mrsiprep.mrsi.resampling mrsiprep.parcellation.chimera_native mrsiprep.parcellation.extraction mrsiprep.parcellation.mni_atlas mrsiprep.parcellation.synthseg mrsiprep.parcellation.tissue_regression mrsiprep.registration.mrsi_to_t1 mrsiprep.registration.subject_template mrsiprep.registration.t1_to_mni mrsiprep.registration.transforms mrsiprep.tissue.fractions mrsiprep.tissue.fuzzy_cmeans mrsiprep.tissue.psf mrsiprep.tissue.synthseg_fast mrsiprep.workflows.anatomical mrsiprep.workflows.base mrsiprep.workflows.connectivity mrsiprep.workflows.mrsi mrsiprep.workflows.parcellation mrsiprep.workflows.participant mrsiprep.workflows.registration mrsiprep.workflows.reports mrsiprep.workflows.tissue mrsi (mrsiprep.workflows.tissue.TissueResult attribute) mrsi_derivative() (in module mrsiprep.io.naming) mrsi_map() (mrsiprep.io.bids.BIDSLayout method) mrsi_parcel_dir() (in module mrsiprep.io.naming) mrsi_to_t1 (mrsiprep.workflows.registration.RegistrationResult attribute) MRSIInputs (class in mrsiprep.io.loaders) mrsiprep.config.defaults module mrsiprep.config.settings module mrsiprep.connectivity.connectivity module mrsiprep.connectivity.export module mrsiprep.interfaces.ants module mrsiprep.interfaces.chimera module mrsiprep.interfaces.freesurfer module mrsiprep.interfaces.fsl module

mrsiprep.io.bids module mrsiprep.io.derivatives module mrsiprep.io.loaders module mrsiprep.io.mrsinmrs module mrsiprep.io.naming module mrsiprep.io.validators module mrsiprep.mrsi.filtering module mrsiprep.mrsi.masks module mrsiprep.mrsi.pvc module mrsiprep.mrsi.quality module mrsiprep.mrsi.reference module mrsiprep.mrsi.resampling module mrsiprep.parcellation.chimera_native module mrsiprep.parcellation.extraction module mrsiprep.parcellation.mni_atlas module mrsiprep.parcellation.synthseg module mrsiprep.parcellation.tissue_regression module mrsiprep.registration.mrsi_to_t1 module mrsiprep.registration.subject_template module mrsiprep.registration.t1_to_mni module mrsiprep.registration.transforms module mrsiprep.tissue.fractions module mrsiprep.tissue.fuzzy_cmeans module mrsiprep.tissue.psf module mrsiprep.tissue.synthseg_fast module mrsiprep.workflows.anatomical module mrsiprep.workflows.base module mrsiprep.workflows.connectivity module mrsiprep.workflows.mrsi module mrsiprep.workflows.parcellation module mrsiprep.workflows.participant module mrsiprep.workflows.registration module mrsiprep.workflows.reports module mrsiprep.workflows.tissue module MRSIPrepConfig (class in mrsiprep.config.settings) MRSIResult (class in mrsiprep.workflows.mrsi) MRSIToT1Result (class in mrsiprep.registration.mrsi_to_t1)

N

n_perturbations (mrsiprep.connectivity.connectivity.ConnectivityResult attribute) (mrsiprep.connectivity.connectivity.MetabolicProfileResult attribute) n_voxels (mrsiprep.parcellation.tissue_regression.RegressionResult attribute)

no_pvc (mrsiprep.config.settings.MRSIPrepConfig attribute) normalization (mrsiprep.config.settings.MRSIPrepConfig attribute) nproc (mrsiprep.config.settings.MRSIPrepConfig attribute) nthreads (mrsiprep.config.settings.MRSIPrepConfig attribute)

O

output_dir (mrsiprep.config.settings.MRSIPrepConfig attribute) output_mrsi_t1w (mrsiprep.config.settings.MRSIPrepConfig attribute) output_spaces (mrsiprep.config.settings.MRSIPrepConfig attribute) outputs (mrsiprep.workflows.participant.RecordingStatus attribute) overwrite (mrsiprep.config.settings.MRSIPrepConfig attribute) overwrite_chimera (mrsiprep.config.settings.MRSIPrepConfig attribute)

overwrite_filt (mrsiprep.config.settings.MRSIPrepConfig attribute) overwrite_mni_reg (mrsiprep.config.settings.MRSIPrepConfig attribute) overwrite_pve (mrsiprep.config.settings.MRSIPrepConfig attribute) overwrite_seg (mrsiprep.config.settings.MRSIPrepConfig attribute) overwrite_t1_reg (mrsiprep.config.settings.MRSIPrepConfig attribute) overwrite_t1corr (mrsiprep.config.settings.MRSIPrepConfig attribute) overwrite_transform (mrsiprep.config.settings.MRSIPrepConfig attribute)

P

parcel_concentrations (mrsiprep.connectivity.connectivity.ConnectivityResult attribute) (mrsiprep.connectivity.connectivity.MetabolicProfileResult attribute) parcel_ids (mrsiprep.connectivity.connectivity.ConnectivityResult attribute) (mrsiprep.connectivity.connectivity.MetabolicProfileResult attribute) parcellate_means() (in module mrsiprep.connectivity.connectivity) parcellate_zscored() (in module mrsiprep.connectivity.connectivity) parcellation_derivative() (in module mrsiprep.io.naming) parcellation_mode (mrsiprep.config.settings.MRSIPrepConfig attribute) participant_label (mrsiprep.config.settings.MRSIPrepConfig attribute) participants_file (mrsiprep.config.settings.MRSIPrepConfig attribute) per_session_forward (mrsiprep.registration.subject_template.SubjectTemplateResult attribute)

perturb_metabolite_map() (in module mrsiprep.connectivity.connectivity) prefix (mrsiprep.io.bids.Recording property) (mrsiprep.registration.mrsi_to_t1.MRSIToT1Result attribute) (mrsiprep.registration.t1_to_mni.T1ToMNIResult attribute) prefix() (in module mrsiprep.io.naming) prepare_anatomical() (in module mrsiprep.workflows.anatomical) preproc_maps (mrsiprep.workflows.mrsi.MRSIResult attribute) preset_citation (mrsiprep.config.settings.MRSIPrepConfig attribute) processing_mode (mrsiprep.config.settings.MRSIPrepConfig attribute) provenance_derivative() (in module mrsiprep.io.naming) psf_axes() (in module mrsiprep.tissue.psf) PVCError

Q

qc_report_derivative() (in module mrsiprep.io.naming) qc_summary (mrsiprep.workflows.mrsi.MRSIResult attribute)

qcmasks (mrsiprep.workflows.mrsi.MRSIResult attribute) quality_metrics (mrsiprep.config.settings.MRSIPrepConfig attribute)

R

r_squared (mrsiprep.parcellation.tissue_regression.RegressionResult attribute) rank_deficient (mrsiprep.parcellation.tissue_regression.RegressionResult attribute) raw_maps (mrsiprep.workflows.mrsi.MRSIResult attribute) raw_t1() (mrsiprep.io.bids.BIDSLayout method) raw_t1w (mrsiprep.workflows.anatomical.AnatomicalResult attribute) Recording (class in mrsiprep.io.bids) RecordingStatus (class in mrsiprep.workflows.participant) ref_met (mrsiprep.config.settings.MRSIPrepConfig attribute) reference (mrsiprep.workflows.mrsi.MRSIResult attribute) regional_summary (mrsiprep.config.settings.MRSIPrepConfig attribute) regional_tissue_regression() (in module mrsiprep.parcellation.tissue_regression) register() (in module mrsiprep.interfaces.ants) (mrsiprep.interfaces.ants.Registration method) register_cli() (in module mrsiprep.interfaces.ants) register_flirt() (in module mrsiprep.interfaces.fsl) register_fnirt() (in module mrsiprep.interfaces.fsl) Registration (class in mrsiprep.interfaces.ants) registration_backend (mrsiprep.config.settings.MRSIPrepConfig attribute) registration_mask (mrsiprep.workflows.anatomical.AnatomicalResult attribute) registration_t1_target (mrsiprep.config.settings.MRSIPrepConfig attribute) registration_t1w (mrsiprep.workflows.anatomical.AnatomicalResult attribute) RegistrationResult (class in mrsiprep.workflows.registration) RegressionResult (class in mrsiprep.parcellation.tissue_regression) require_cli() (in module mrsiprep.interfaces.ants) (in module mrsiprep.interfaces.fsl) require_command() (in module mrsiprep.interfaces.freesurfer)

resample_ref_met_to_t1w() (in module mrsiprep.mrsi.resampling) resample_tissue_to_mrsi() (in module mrsiprep.tissue.fractions) resample_tissue_to_mrsi_psf() (in module mrsiprep.tissue.psf) resampling_work_path() (in module mrsiprep.io.naming) resolve_cpu_budget() (mrsiprep.config.settings.MRSIPrepConfig method) resolve_mrsinmrs() (in module mrsiprep.io.mrsinmrs) run_chimera() (in module mrsiprep.interfaces.chimera) run_chimera_parcellation() (in module mrsiprep.parcellation.chimera_native) run_cli() (in module mrsiprep.interfaces.ants) (in module mrsiprep.interfaces.fsl) run_connectivity_workflow() (in module mrsiprep.workflows.connectivity) run_fast() (in module mrsiprep.interfaces.fsl) run_mni_parcellation() (in module mrsiprep.parcellation.mni_atlas) run_mrsi_to_t1() (in module mrsiprep.registration.mrsi_to_t1) run_mrsi_to_t1_rigid_mi() (in module mrsiprep.registration.mrsi_to_t1) run_mrsi_workflow() (in module mrsiprep.workflows.mrsi) run_or_load_synthseg_labels() (in module mrsiprep.tissue.synthseg_fast) run_parcellation_workflow() (in module mrsiprep.workflows.parcellation) run_participant_workflow() (in module mrsiprep.workflows.participant) run_pvc() (in module mrsiprep.mrsi.pvc) run_recon_all() (in module mrsiprep.interfaces.freesurfer) run_registration_workflow() (in module mrsiprep.workflows.registration) run_reports_workflow() (in module mrsiprep.workflows.reports) run_synthseg_parcellation() (in module mrsiprep.parcellation.synthseg) run_t1_to_mni() (in module mrsiprep.registration.t1_to_mni) run_tissue_workflow() (in module mrsiprep.workflows.tissue)

S

save_all_transforms() (in module mrsiprep.interfaces.ants) (mrsiprep.interfaces.ants.Registration method) se_gm (mrsiprep.parcellation.tissue_regression.RegressionResult attribute) se_wm (mrsiprep.parcellation.tissue_regression.RegressionResult attribute) segment_t1_fuzzy_cmeans() (in module mrsiprep.workflows.tissue) segment_t1_synthseg_fast() (in module mrsiprep.tissue.synthseg_fast) session (mrsiprep.io.bids.Recording attribute) (mrsiprep.workflows.participant.RecordingStatus attribute) session_label (mrsiprep.config.settings.MRSIPrepConfig attribute) sigma_scale (mrsiprep.connectivity.connectivity.ConnectivityResult attribute) (mrsiprep.connectivity.connectivity.MetabolicProfileResult attribute) similarity (mrsiprep.connectivity.connectivity.ConnectivityResult attribute) skip_file_integrity_check (mrsiprep.config.settings.MRSIPrepConfig attribute) snr_map (mrsiprep.io.loaders.MRSIInputs attribute) (mrsiprep.workflows.mrsi.MRSIResult attribute) snr_min (mrsiprep.config.settings.MRSIPrepConfig attribute)

spike_max_cluster_voxels (mrsiprep.config.settings.MRSIPrepConfig attribute) spike_percentile (mrsiprep.config.settings.MRSIPrepConfig attribute) status (mrsiprep.workflows.participant.RecordingStatus attribute) stop_on_first_crash (mrsiprep.config.settings.MRSIPrepConfig attribute) subject (mrsiprep.io.bids.Recording attribute) (mrsiprep.workflows.participant.RecordingStatus attribute) subject_dir_valid() (in module mrsiprep.interfaces.freesurfer) subject_session_dir() (in module mrsiprep.io.naming) SubjectTemplateResult (class in mrsiprep.registration.subject_template) synthseg_fast_brain_mask_path() (in module mrsiprep.tissue.synthseg_fast) synthseg_fast_brain_path() (in module mrsiprep.tissue.synthseg_fast) synthseg_fast_csf_probseg_path() (in module mrsiprep.tissue.synthseg_fast) synthseg_fast_input_path() (in module mrsiprep.tissue.synthseg_fast) synthseg_mode (mrsiprep.config.settings.MRSIPrepConfig attribute) synthseg_native_labels_path() (in module mrsiprep.tissue.synthseg_fast) synthseg_work_dir() (in module mrsiprep.tissue.synthseg_fast)

T

t1 (mrsiprep.workflows.tissue.TissueResult attribute) t1() (mrsiprep.io.bids.BIDSLayout method) t1_correction (mrsiprep.config.settings.MRSIPrepConfig attribute) t1_correction_provenance (mrsiprep.workflows.mrsi.MRSIResult attribute) t1_correction_water_status (mrsiprep.config.settings.MRSIPrepConfig attribute) t1_pattern (mrsiprep.config.settings.MRSIPrepConfig attribute) t1_to_mni (mrsiprep.workflows.registration.RegistrationResult attribute) T1ToMNIResult (class in mrsiprep.registration.t1_to_mni) t1w (mrsiprep.workflows.anatomical.AnatomicalResult attribute) target_kind (mrsiprep.workflows.anatomical.AnatomicalResult attribute) template (mrsiprep.registration.t1_to_mni.T1ToMNIResult attribute)

template_path (mrsiprep.registration.subject_template.SubjectTemplateResult attribute) template_to_mni_forward (mrsiprep.registration.subject_template.SubjectTemplateResult attribute) template_to_mni_inverse (mrsiprep.registration.subject_template.SubjectTemplateResult attribute) tissue_backend (mrsiprep.config.settings.MRSIPrepConfig attribute) TissueResult (class in mrsiprep.workflows.tissue) to_dict() (mrsiprep.config.settings.MRSIPrepConfig method) transform (mrsiprep.config.settings.MRSIPrepConfig attribute) transform() (mrsiprep.interfaces.ants.Registration method) (mrsiprep.io.bids.BIDSLayout method) transform_mrsi_maps() (in module mrsiprep.mrsi.resampling) transform_paths() (in module mrsiprep.registration.transforms) transform_spikemask (mrsiprep.config.settings.MRSIPrepConfig attribute)

V

validate_only (mrsiprep.config.settings.MRSIPrepConfig attribute) validate_participant_inputs() (in module mrsiprep.workflows.participant)

validate_recording() (in module mrsiprep.io.validators) ValidationError verbose (mrsiprep.config.settings.MRSIPrepConfig attribute)

W

water_map (mrsiprep.io.loaders.MRSIInputs attribute) (mrsiprep.workflows.mrsi.MRSIResult attribute)

work_dir (mrsiprep.config.settings.MRSIPrepConfig attribute) write_connectivity (mrsiprep.config.settings.MRSIPrepConfig attribute)