Index

_

__init__() (qsiprep.interfaces.denoise.SeriesPreprocReport method) (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit method) (qsiprep.utils.brainsuite_shore.BrainSuiteShoreModel method)

A

aattp_rotate_vec() (in module qsiprep.interfaces.gradients) AboutSummary (class in qsiprep.interfaces) (class in qsiprep.interfaces.reports) ACPCReport (class in qsiprep.interfaces.itk) add_epi_fmaps_to_dwi_b0s() (in module qsiprep.interfaces.fmap) add_suffix() (in module qsiprep.utils.misc) AddTSVHeader (class in qsiprep.interfaces) (class in qsiprep.interfaces.utils) AffineToRigid (class in qsiprep.interfaces.itk) age_to_months() (in module qsiprep.utils.bids) alpha (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit property) anat_modality (qsiprep.config.workflow attribute), [1], [2]

anat_only (qsiprep.config.workflow attribute), [1], [2] anatomical_template (qsiprep.config.workflow attribute), [1], [2] angle_between() (in module qsiprep.interfaces.dwi_merge) anisotropic_power() (in module qsiprep.utils.shm) ants (qsiprep.config.seeds attribute) ANTSRegistrationRPT (class in qsiprep.interfaces.niworkflows) ApplyScalingImages (class in qsiprep.interfaces.fmap) as_path() (in module qsiprep.utils.resources) average_bvec() (in module qsiprep.interfaces.dwi_merge) average_carpetplots() (in module qsiprep.interfaces.dwi_merge) average_image_pairs() (in module qsiprep.interfaces.dwi_merge) AveragePEPairs (class in qsiprep.interfaces.dwi_merge)

B

b0_motion_corr_to (qsiprep.config.workflow attribute), [1], [2] b0_threshold (qsiprep.config.workflow attribute), [1], [2] b0_to_t1w_transform (qsiprep.config.workflow attribute), [1], [2] B0Mean (class in qsiprep.interfaces.shoreline) B0RPEFieldmap (class in qsiprep.interfaces.fmap) b1_biascorrect_stage (qsiprep.config.workflow attribute), [1], [2] before_after_images() (in module qsiprep.interfaces.shoreline) before_send() (in module qsiprep.utils.sentry) biascorrect() (in module qsiprep.interfaces.nilearn) bids_database_dir (qsiprep.config.execution attribute), [1], [2] bids_description_hash (qsiprep.config.execution attribute), [1], [2] bids_dir (qsiprep.config.execution attribute), [1], [2] bids_filters (qsiprep.config.execution attribute), [1], [2] BIDSDataGrabber (class in qsiprep.interfaces) (class in qsiprep.interfaces.bids) BIDSError

BIDSInfo (class in qsiprep.interfaces) (class in qsiprep.interfaces.bids) BIDSWarning boilerplate_from_eddy_config() (in module qsiprep.interfaces.eddy) boilerplate_only (qsiprep.config.execution attribute), [1], [2] bootstrap_data_array() (in module qsiprep.utils.shm) bootstrap_data_voxel() (in module qsiprep.utils.shm) brainsuite_shore_basis() (in module qsiprep.utils.brainsuite_shore) brainsuite_shore_matrix_pdf() (in module qsiprep.utils.brainsuite_shore) BrainSuiteShoreFit (class in qsiprep.utils.brainsuite_shore) BrainSuiteShoreModel (class in qsiprep.utils.brainsuite_shore) btable_from_bvals_bvecs() (in module qsiprep.interfaces.dsi_studio) build_boilerplate() (in module qsiprep.cli.workflow) build_workflow() (in module qsiprep.cli.workflow) bvec_rotation() (in module qsiprep.interfaces.gradients) bvec_to_rasb() (in module qsiprep.interfaces.images)

C

calculate_best_b0s() (in module qsiprep.interfaces.epi_fmap) calculate_gradmax_b0_mask() (in module qsiprep.interfaces.nilearn) calculate_max_order() (in module qsiprep.utils.shm) calculate_motion_summary() (in module qsiprep.interfaces.reports) calculate_nonbrain_saturation() (in module qsiprep.interfaces.anatomical) CalculateCNR (class in qsiprep.interfaces.shoreline) check_deps() (in module qsiprep.utils) (in module qsiprep.utils.misc) check_latest() (in module qsiprep.cli.version) ChooseInterpolator (class in qsiprep.interfaces.images) cleanup_edge_pipeline() (in module qsiprep.workflows.fieldmap.utils) cli (qsiprep.config.loggers attribute), [1], [2] closest_odd() (in module qsiprep.workflows.dwi.merge) cmdline (qsiprep.interfaces.freesurfer.StructuralReference property) (qsiprep.interfaces.StructuralReference property) cnr (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit property) cohort_by_months() (in module qsiprep.utils.bids) collect_data() (in module qsiprep.utils) (in module qsiprep.utils.bids) collect_participants() (in module qsiprep.utils.bids) combine_bvals() (in module qsiprep.interfaces.dwi_merge) combine_bvecs() (in module qsiprep.interfaces.dwi_merge) combine_metadata() (in module qsiprep.interfaces.dwi_merge) combined_bval_array() (in module qsiprep.interfaces.dwi_merge) combined_bvec_array() (in module qsiprep.interfaces.dwi_merge)

CombineMotions (class in qsiprep.interfaces.gradients) ComplexToMagnitude (class in qsiprep.interfaces.mrtrix) compose_affines() (in module qsiprep.interfaces.gradients) (in module qsiprep.interfaces.itk) ComposeTransforms (class in qsiprep.interfaces.gradients) compute_affine() (in module qsiprep.utils.bspline) ConcatAffines (class in qsiprep.interfaces) (class in qsiprep.interfaces.utils) concatenate_bvals() (in module qsiprep.interfaces.gradients) concatenate_bvecs() (in module qsiprep.interfaces.gradients) Conform (class in qsiprep.interfaces) (class in qsiprep.interfaces.images), [1] ConformDwi (class in qsiprep.interfaces) (class in qsiprep.interfaces.images) confoundplot() (in module qsiprep.interfaces.niworkflows) ConvertTransformFile (class in qsiprep.interfaces.ants) cpu_count (qsiprep.config.environment attribute), [1], [2] crashfile_format (qsiprep.config.nipype attribute), [1], [2] create_provenance_dataframe() (in module qsiprep.interfaces.dwi_merge) create_report_json() (in module qsiprep.interfaces.qc) create_rspace() (in module qsiprep.utils.brainsuite_shore) create_sprite_from_tiles() (in module qsiprep.interfaces.qc) create_tensor_image() (in module qsiprep.interfaces.gradients) createB0_ColorFA_Mask_Sprites() (in module qsiprep.interfaces.qc) createSprite4D() (in module qsiprep.interfaces.qc)

D

dataset_links (qsiprep.config.execution attribute), [1], [2] debug (qsiprep.config.execution attribute), [1], [2] default (qsiprep.config.loggers attribute), [1], [2] demean_image() (in module qsiprep.workflows.fieldmap.utils) denoise_after_combining (qsiprep.config.workflow attribute), [1], [2] denoise_method (qsiprep.config.workflow attribute), [1], [2] derivatives (qsiprep.config.execution attribute), [1], [2] DerivativesDataSink (class in qsiprep.interfaces) (class in qsiprep.interfaces.bids) DerivativesMaybeDataSink (class in qsiprep.interfaces) (class in qsiprep.interfaces.bids) DerivativesSidecar (class in qsiprep.interfaces.bids) DesaturateSkull (class in qsiprep.interfaces.anatomical) DiceOverlap (class in qsiprep.interfaces.anatomical) DiffusionSummary (class in qsiprep.interfaces.reports) disassemble_transform() (in module qsiprep.interfaces.itk) DisassembleTransform (class in qsiprep.interfaces.itk) distortion_group_merge (qsiprep.config.workflow attribute), [1], [2]

dMRIPlot (class in qsiprep.interfaces.niworkflows) DMRISummary (class in qsiprep.interfaces) (class in qsiprep.interfaces.confounds) DRBUDDI (class in qsiprep.interfaces.tortoise) DRBUDDIAggregateOutputs (class in qsiprep.interfaces.tortoise) DSIStudioBTable (class in qsiprep.interfaces.dsi_studio) DSIStudioCreateSrc (class in qsiprep.interfaces.dsi_studio) DSIStudioFibQC (class in qsiprep.interfaces.dsi_studio) DSIStudioGQIReconstruction (class in qsiprep.interfaces.dsi_studio) DSIStudioMergeQC (class in qsiprep.interfaces.dsi_studio) DSIStudioQC (class in qsiprep.interfaces.dsi_studio) DSIStudioSrcQC (class in qsiprep.interfaces.dsi_studio) dumps() (in module qsiprep.config), [1] dwi_denoise_window (qsiprep.config.workflow attribute), [1], [2] dwi_no_biascorr (qsiprep.config.workflow attribute), [1], [2] dwi_only (qsiprep.config.workflow attribute), [1], [2] DWIBiasCorrect (class in qsiprep.interfaces.mrtrix) DWIDenoise (class in qsiprep.interfaces.mrtrix)

E

Eddy2SPMMotion (class in qsiprep.interfaces.eddy) eddy_config (qsiprep.config.workflow attribute), [1], [2] eddy_inputs_from_dwi_files() (in module qsiprep.interfaces.epi_fmap) (in module qsiprep.interfaces.fmap) embed_tiles_in_json_sprite() (in module qsiprep.interfaces.qc) EnhanceB0 (class in qsiprep.interfaces.nilearn) environment (class in qsiprep.config), [1], [2] exec_docker_version (qsiprep.config.environment attribute), [1], [2]

exec_env (qsiprep.config.environment attribute), [1], [2] execution (class in qsiprep.config), [1], [2] ext (qsiprep.interfaces.dsi_studio.DSIStudioFibQC attribute) (qsiprep.interfaces.dsi_studio.DSIStudioSrcQC attribute) ExtendedEddy (class in qsiprep.interfaces.eddy) ExtractB0s (class in qsiprep.interfaces.gradients) ExtractDWIsForModel (class in qsiprep.interfaces.shoreline) ExtractWM (class in qsiprep.interfaces.images)

F

FakeSegmentation (class in qsiprep.interfaces.anatomical) FieldToHz (class in qsiprep.interfaces) (class in qsiprep.interfaces.fmap) FieldToRadS (class in qsiprep.interfaces) (class in qsiprep.interfaces.fmap) FileNotFoundError find_fieldmaps_from_other_dwis() (in module qsiprep.utils.grouping) find_image_pairs() (in module qsiprep.interfaces.dwi_merge) first_image() (in module qsiprep.workflows.dwi.hmc) fit() (qsiprep.utils.brainsuite_shore.BrainSuiteShoreModel method)

fitted_signal() (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit method) fix_multi_source_name() (in module qsiprep.utils.misc) fix_multi_T1w_source_name() (in module qsiprep.utils.misc) FixHeaderSynthStrip (class in qsiprep.interfaces.freesurfer) fmap_bspline (qsiprep.config.workflow attribute), [1], [2] fmap_demean (qsiprep.config.workflow attribute), [1], [2] force_syn (qsiprep.config.workflow attribute), [1], [2] forward_sdeconv_mat() (in module qsiprep.utils.shm) free_mem (qsiprep.config.environment attribute), [1], [2] from_dict() (in module qsiprep.config), [1] FUGUEvsm2ANTSwarp (class in qsiprep.interfaces.niworkflows)

G

GatherConfounds (class in qsiprep.interfaces) (class in qsiprep.interfaces.confounds) GatherDRBUDDIInputs (class in qsiprep.interfaces.tortoise) GatherEddyInputs (class in qsiprep.interfaces.eddy) gen_denoising_boilerplate() (in module qsiprep.workflows.dwi.merge) gen_dirac() (in module qsiprep.utils.shm) generate_drbuddi_boilerplate() (in module qsiprep.interfaces.tortoise) get() (in module qsiprep.config), [1] get_acq_parameters_df() (in module qsiprep.workflows.dwi.merge) get_best_b0_topup_inputs_from() (in module qsiprep.interfaces.epi_fmap) get_bids_params() (in module qsiprep.interfaces.bids) get_cnr_values() (in module qsiprep.interfaces.reports) get_concatenated_bids_name() (in module qsiprep.utils.grouping) get_distortion_grouping() (in module qsiprep.interfaces.epi_fmap) (in module qsiprep.interfaces.fmap) get_ees() (in module qsiprep.interfaces.fmap) get_entity_groups() (in module qsiprep.utils.grouping) get_evenly_spaced_b0s() (in module qsiprep.interfaces.fmap) get_fieldmap_values() (in module qsiprep.interfaces.reports) get_fsl_motion_params() (in module qsiprep.interfaces.gradients) get_grouping_test_data() (in module qsiprep.utils.testing)

get_highest_priority_fieldmap() (in module qsiprep.utils.grouping) get_ijk() (in module qsiprep.utils.bspline) get_linked_libs (qsiprep.config.nipype attribute), [1], [2] get_merged_parameter() (in module qsiprep.workflows.dwi.merge) get_middle_slice_tiles() (in module qsiprep.interfaces.qc) get_nvols() (in module qsiprep.interfaces.dwi_merge) get_plugin() (qsiprep.config.nipype class method), [1], [2] get_source_file() (in module qsiprep.workflows.dwi.util) get_topup_inputs_from() (in module qsiprep.interfaces.fmap) get_trt() (in module qsiprep.interfaces.fmap) get_vector_nii() (in module qsiprep.interfaces.gradients) get_worst() (in module qsiprep.interfaces.dwi_merge) GetImageType (class in qsiprep.interfaces.ants) GetTemplate (class in qsiprep.interfaces.anatomical) gfa() (qsiprep.utils.shm.SphHarmFit method) Gibbs (class in qsiprep.interfaces.tortoise) GradientPlot (class in qsiprep.interfaces.reports) GradientRotation (class in qsiprep.interfaces.gradients) group_by_warpspace() (in module qsiprep.utils.grouping) group_dwi_scans() (in module qsiprep.utils.grouping) group_for_eddy() (in module qsiprep.utils.grouping)

H

harmonize_b0s() (in module qsiprep.interfaces.dwi_merge) hat() (in module qsiprep.utils.shm)

hmc_model (qsiprep.config.workflow attribute), [1], [2] hmc_transform (qsiprep.config.workflow attribute), [1], [2]

I

ignore (qsiprep.config.workflow attribute), [1], [2] ImageMath (class in qsiprep.interfaces.ants) infant (qsiprep.config.workflow attribute), [1], [2] init() (qsiprep.config.execution class method), [1], [2] (qsiprep.config.loggers class method), [1], [2] (qsiprep.config.nipype class method), [1], [2] (qsiprep.config.seeds class method) init_anat_derivatives_wf() (in module qsiprep.workflows.anatomical.volume) init_anat_normalization_wf() (in module qsiprep.workflows.anatomical.volume) init_anat_preproc_wf() (in module qsiprep.workflows.anatomical) (in module qsiprep.workflows.anatomical.volume), [1] init_anat_reports_wf() (in module qsiprep.workflows.anatomical.volume) init_anat_template_wf() (in module qsiprep.workflows.anatomical.volume) init_b0_hmc_wf() (in module qsiprep.workflows.dwi.hmc) init_b0_to_anat_registration_wf() (in module qsiprep.workflows.dwi.registration) init_direct_b0_acpc_wf() (in module qsiprep.workflows.dwi.registration) init_distortion_group_merge_wf() (in module qsiprep.workflows.dwi.distortion_group_merge) init_dl_prep_wf() (in module qsiprep.workflows.anatomical.volume) init_drbuddi_wf() (in module qsiprep.workflows.fieldmap) (in module qsiprep.workflows.fieldmap.drbuddi) init_dwi_confs_wf() (in module qsiprep.workflows.dwi.confounds), [1], [2] init_dwi_denoising_wf() (in module qsiprep.workflows.dwi.merge) init_dwi_derivatives_wf() (in module qsiprep.workflows.dwi.derivatives), [1] init_dwi_finalize_wf() (in module qsiprep.workflows.dwi.finalize), [1] init_dwi_hmc_wf() (in module qsiprep.workflows.dwi.hmc), [1], [2] init_dwi_model_hmc_wf() (in module qsiprep.workflows.dwi.hmc), [1], [2] init_dwi_pre_hmc_wf() (in module qsiprep.workflows.dwi.pre_hmc) init_dwi_preproc_wf() (in module qsiprep.workflows.dwi.base), [1], [2] init_dwi_reference_wf() (in module qsiprep.workflows.dwi.util), [1], [2] init_dwi_trans_wf() (in module qsiprep.workflows.dwi.resampling), [1], [2] init_extended_pepolar_report_wf() (in module qsiprep.workflows.fieldmap.pepolar), [1] init_finalize_denoising_wf() (in module qsiprep.workflows.dwi.finalize) init_fmap_unwarp_report_wf() (in module qsiprep.workflows.fieldmap) (in module qsiprep.workflows.fieldmap.unwarp), [1] init_fmap_wf() (in module qsiprep.workflows.fieldmap.fmap), [1] init_fsl_hmc_wf() (in module qsiprep.workflows.dwi.fsl), [1], [2]

init_hmc_model_iteration_wf() (in module qsiprep.workflows.dwi.hmc) init_intramodal_template_wf() (in module qsiprep.workflows.dwi.intramodal_template) init_mask_overlap_wf() (in module qsiprep.workflows.dwi.qc) init_merge_and_denoise_wf() (in module qsiprep.workflows.dwi.merge) init_modelfree_qc_wf() (in module qsiprep.workflows.dwi.qc) init_nonlinear_alignment_wf() (in module qsiprep.workflows.dwi.intramodal_template) init_output_grid_wf() (in module qsiprep.workflows.anatomical.volume) init_pepolar_unwarp_wf() (in module qsiprep.workflows.fieldmap) (in module qsiprep.workflows.fieldmap.pepolar), [1] init_phdiff_wf() (in module qsiprep.workflows.fieldmap.phdiff), [1] init_prepare_dwi_epi_wf() (in module qsiprep.workflows.fieldmap.pepolar), [1] init_qsiprep_hmcsdc_wf() (in module qsiprep.workflows.dwi.hmc_sdc) init_qsiprep_intramodal_template_wf() (in module qsiprep.workflows.dwi.intramodal_template) init_qsiprep_wf() (in module qsiprep.workflows.base), [1] init_sdc_unwarp_wf() (in module qsiprep.workflows.fieldmap) (in module qsiprep.workflows.fieldmap.unwarp), [1] init_sdc_wf() (in module qsiprep.workflows.fieldmap) (in module qsiprep.workflows.fieldmap.base), [1] init_single_subject_wf() (in module qsiprep.workflows.base), [1] init_spaces() (in module qsiprep.config), [1] init_syn_sdc_wf() (in module qsiprep.workflows.fieldmap) (in module qsiprep.workflows.fieldmap.syn), [1] init_synthseg_wf() (in module qsiprep.workflows.anatomical) (in module qsiprep.workflows.anatomical.volume) init_synthstrip_wf() (in module qsiprep.workflows.anatomical) (in module qsiprep.workflows.anatomical.volume) init_t2w_preproc_wf() (in module qsiprep.workflows.anatomical.volume) interface (qsiprep.config.loggers attribute), [1], [2] intramodal_template_iters (qsiprep.config.workflow attribute), [1], [2] intramodal_template_transform (qsiprep.config.workflow attribute), [1], [2] IntraModalMerge (class in qsiprep.interfaces) (class in qsiprep.interfaces.images) is_flagged() (in module qsiprep.cli.version) is_interactive() (in module qsiprep.utils.debug) IterationSummary (class in qsiprep.interfaces.shoreline) itk_affine_to_rigid() (in module qsiprep.interfaces.itk) ITKTransformConvert (class in qsiprep.interfaces.mrtrix)

L

layout (qsiprep.config.execution attribute), [1], [2] lazy_index() (in module qsiprep.utils.shm) lcr_matrix() (in module qsiprep.utils.shm) linear_alignment_workflow() (in module qsiprep.workflows.dwi.hmc) load() (in module qsiprep.config), [1] load_and_reorient() (in module qsiprep.interfaces.qc) load_epi_dwi_fieldmaps() (in module qsiprep.interfaces.epi_fmap) (in module qsiprep.interfaces.fmap)

load_fib_qc_file() (in module qsiprep.interfaces.dsi_studio) load_src_qc_file() (in module qsiprep.interfaces.dsi_studio) local_bvec_rotation() (in module qsiprep.interfaces.gradients) LocalGradientRotation (class in qsiprep.interfaces.gradients) log_dir (qsiprep.config.execution attribute), [1], [2] log_level (qsiprep.config.execution attribute), [1], [2] loggers (class in qsiprep.config), [1], [2] longitudinal (qsiprep.config.workflow attribute), [1], [2] low_mem (qsiprep.config.execution attribute), [1], [2]

M

main() (in module qsiprep.cli.run) make_a_square() (in module qsiprep.interfaces.qc) make_bmat_file() (in module qsiprep.interfaces.tortoise) MaskEPI (class in qsiprep.interfaces.nilearn) master (qsiprep.config.seeds attribute) match_transforms() (in module qsiprep.interfaces.gradients) MatchTransforms (class in qsiprep.interfaces.gradients) memory_gb (qsiprep.config.nipype attribute), [1], [2] Merge (class in qsiprep.interfaces.nilearn) merge_dwi_groups() (in module qsiprep.utils.grouping) MergeDWIs (class in qsiprep.interfaces.dwi_merge) MergeFinalConfounds (class in qsiprep.interfaces.dwi_merge) MockSynthSeg (class in qsiprep.interfaces.freesurfer) MockSynthStrip (class in qsiprep.interfaces.freesurfer) module qsiprep qsiprep.cli qsiprep.cli.parser qsiprep.cli.run qsiprep.cli.version qsiprep.cli.workflow qsiprep.config, [1] qsiprep.interfaces qsiprep.interfaces.anatomical qsiprep.interfaces.ants qsiprep.interfaces.bids qsiprep.interfaces.confounds qsiprep.interfaces.denoise qsiprep.interfaces.dipy qsiprep.interfaces.dsi_studio qsiprep.interfaces.dwi_merge qsiprep.interfaces.eddy qsiprep.interfaces.epi_fmap qsiprep.interfaces.fmap qsiprep.interfaces.freesurfer qsiprep.interfaces.gradients qsiprep.interfaces.images qsiprep.interfaces.itk qsiprep.interfaces.mrtrix qsiprep.interfaces.nilearn qsiprep.interfaces.niworkflows qsiprep.interfaces.qc qsiprep.interfaces.reports qsiprep.interfaces.shoreline qsiprep.interfaces.tortoise qsiprep.interfaces.utils qsiprep.utils qsiprep.utils.bids qsiprep.utils.brainsuite_shore qsiprep.utils.bspline qsiprep.utils.debug qsiprep.utils.grouping qsiprep.utils.misc qsiprep.utils.resources qsiprep.utils.sentry qsiprep.utils.shm qsiprep.utils.testing qsiprep.viz qsiprep.viz.utils qsiprep.workflows qsiprep.workflows.anatomical qsiprep.workflows.anatomical.volume qsiprep.workflows.base qsiprep.workflows.dwi qsiprep.workflows.dwi.base, [1] qsiprep.workflows.dwi.confounds, [1] qsiprep.workflows.dwi.derivatives qsiprep.workflows.dwi.distortion_group_merge qsiprep.workflows.dwi.finalize qsiprep.workflows.dwi.fsl, [1] qsiprep.workflows.dwi.hmc, [1] qsiprep.workflows.dwi.hmc_sdc qsiprep.workflows.dwi.intramodal_template qsiprep.workflows.dwi.merge qsiprep.workflows.dwi.pre_hmc qsiprep.workflows.dwi.qc qsiprep.workflows.dwi.registration, [1] qsiprep.workflows.dwi.resampling, [1] qsiprep.workflows.dwi.util, [1] qsiprep.workflows.fieldmap qsiprep.workflows.fieldmap.base, [1] qsiprep.workflows.fieldmap.drbuddi qsiprep.workflows.fieldmap.fmap, [1] qsiprep.workflows.fieldmap.pepolar, [1] qsiprep.workflows.fieldmap.phdiff, [1] qsiprep.workflows.fieldmap.syn, [1] qsiprep.workflows.fieldmap.unwarp, [1] qsiprep.workflows.fieldmap.utils

motion_derivatives() (in module qsiprep.interfaces.reports) mplfig() (in module qsiprep.interfaces.qc) mplfigcontour() (in module qsiprep.interfaces.qc) MRDeGibbs (class in qsiprep.interfaces.mrtrix) MRTrixGradientTable (class in qsiprep.interfaces.mrtrix) MRTrixIngress (class in qsiprep.interfaces.mrtrix) msd() (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit method) MultivariateTemplateConstruction2 (class in qsiprep.interfaces.ants)

N

nearest_square() (in module qsiprep.interfaces.qc) nipype (class in qsiprep.config), [1], [2] nipype_version (qsiprep.config.environment attribute), [1], [2] no_b0_harmonization (qsiprep.config.workflow attribute), [1], [2]

nonlinear_alignment_iteration() (in module qsiprep.workflows.dwi.intramodal_template) normalize_data() (in module qsiprep.utils.shm) notrack (qsiprep.config.execution attribute), [1], [2] nprocs (qsiprep.config.nipype attribute), [1], [2] numpy (qsiprep.config.seeds attribute)

O

odf() (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit method) (qsiprep.utils.shm.SphHarmFit method) odf_sh() (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit method) omp_nthreads (qsiprep.config.nipype attribute), [1], [2] order_from_ncoef() (in module qsiprep.utils.shm) out_path_base (qsiprep.interfaces.bids.DerivativesDataSink attribute) (qsiprep.interfaces.DerivativesDataSink attribute)

output_dir (qsiprep.config.execution attribute), [1], [2] output_layout (qsiprep.config.execution attribute), [1], [2] output_resolution (qsiprep.config.workflow attribute), [1], [2] overcommit_limit (qsiprep.config.environment attribute), [1], [2] overcommit_policy (qsiprep.config.environment attribute), [1], [2]

P

ParallelTOPUP (class in qsiprep.interfaces.fmap) parse_args() (in module qsiprep.cli.parser) parse_bids_for_age_months() (in module qsiprep.utils.bids) participant_label (qsiprep.config.execution attribute), [1], [2] Patch2Self (class in qsiprep.interfaces.dipy) pdf() (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit method) pdf_grid() (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit method) pepolar_method (qsiprep.config.workflow attribute), [1], [2] PEPOLARReport (class in qsiprep.interfaces.fmap) Phasediff2Fieldmap (class in qsiprep.interfaces) (class in qsiprep.interfaces.fmap) Phases2Fieldmap (class in qsiprep.interfaces) (class in qsiprep.interfaces.fmap) phases2fmap() (in module qsiprep.interfaces.fmap) PhaseToRad (class in qsiprep.interfaces.dwi_merge) phdiff2fmap() (in module qsiprep.interfaces.fmap)

plot() (qsiprep.interfaces.niworkflows.dMRIPlot method) plot_acpc() (in module qsiprep.viz.utils) plot_denoise() (in module qsiprep.viz.utils) plot_fa_reg() (in module qsiprep.interfaces.fmap) plot_gradients() (in module qsiprep.interfaces.reports) plot_pepolar() (in module qsiprep.interfaces.fmap) plot_sliceqc() (in module qsiprep.interfaces.niworkflows) plugin (qsiprep.config.nipype attribute), [1], [2] plugin_args (qsiprep.config.nipype attribute), [1], [2] PolarToComplex (class in qsiprep.interfaces.mrtrix) popen_run() (in module qsiprep.interfaces.dipy) predict() (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit method) (qsiprep.utils.shm.SphHarmFit method) PrepareSynthStripGrid (class in qsiprep.interfaces.freesurfer) process_crashfile() (in module qsiprep.utils.sentry) processing_list (qsiprep.config.execution attribute), [1], [2] provide_processing_advice() (in module qsiprep.workflows.base)

Q

qsiprep module qsiprep.cli module qsiprep.cli.parser module qsiprep.cli.run module qsiprep.cli.version module qsiprep.cli.workflow module qsiprep.config module, [1] qsiprep.interfaces module qsiprep.interfaces.anatomical module qsiprep.interfaces.ants module qsiprep.interfaces.bids module qsiprep.interfaces.confounds module qsiprep.interfaces.denoise module qsiprep.interfaces.dipy module qsiprep.interfaces.dsi_studio module qsiprep.interfaces.dwi_merge module qsiprep.interfaces.eddy module qsiprep.interfaces.epi_fmap module qsiprep.interfaces.fmap module qsiprep.interfaces.freesurfer module qsiprep.interfaces.gradients module qsiprep.interfaces.images module qsiprep.interfaces.itk module qsiprep.interfaces.mrtrix module qsiprep.interfaces.nilearn module qsiprep.interfaces.niworkflows module qsiprep.interfaces.qc module qsiprep.interfaces.reports module qsiprep.interfaces.shoreline module qsiprep.interfaces.tortoise module qsiprep.interfaces.utils module qsiprep.utils module qsiprep.utils.bids module qsiprep.utils.brainsuite_shore module qsiprep.utils.bspline module qsiprep.utils.debug module qsiprep.utils.grouping module

qsiprep.utils.misc module qsiprep.utils.resources module qsiprep.utils.sentry module qsiprep.utils.shm module qsiprep.utils.testing module qsiprep.viz module qsiprep.viz.utils module qsiprep.workflows module qsiprep.workflows.anatomical module qsiprep.workflows.anatomical.volume module qsiprep.workflows.base module qsiprep.workflows.dwi module qsiprep.workflows.dwi.base module, [1] qsiprep.workflows.dwi.confounds module, [1] qsiprep.workflows.dwi.derivatives module qsiprep.workflows.dwi.distortion_group_merge module qsiprep.workflows.dwi.finalize module qsiprep.workflows.dwi.fsl module, [1] qsiprep.workflows.dwi.hmc module, [1] qsiprep.workflows.dwi.hmc_sdc module qsiprep.workflows.dwi.intramodal_template module qsiprep.workflows.dwi.merge module qsiprep.workflows.dwi.pre_hmc module qsiprep.workflows.dwi.qc module qsiprep.workflows.dwi.registration module, [1] qsiprep.workflows.dwi.resampling module, [1] qsiprep.workflows.dwi.util module, [1] qsiprep.workflows.fieldmap module qsiprep.workflows.fieldmap.base module, [1] qsiprep.workflows.fieldmap.drbuddi module qsiprep.workflows.fieldmap.fmap module, [1] qsiprep.workflows.fieldmap.pepolar module, [1] qsiprep.workflows.fieldmap.phdiff module, [1] qsiprep.workflows.fieldmap.syn module, [1] qsiprep.workflows.fieldmap.unwarp module, [1] qsiprep.workflows.fieldmap.utils module quick_load_images() (in module qsiprep.interfaces.shoreline)

R

r2 (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit property) randint() (in module qsiprep.utils.shm) read_nifti_sidecar() (in module qsiprep.interfaces.epi_fmap) (in module qsiprep.interfaces.fmap) real_sph_harm() (in module qsiprep.utils.shm) real_sym_sh_basis() (in module qsiprep.utils.shm) real_sym_sh_brainsuite() (in module qsiprep.utils.shm) real_sym_sh_mrtrix() (in module qsiprep.utils.shm) regularization (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit property) relative_b0_index() (in module qsiprep.interfaces.epi_fmap) remove_unnecessary_outputs (qsiprep.config.nipype attribute), [1], [2] RemoveDuplicates (class in qsiprep.interfaces.gradients)

ReorderOutputs (class in qsiprep.interfaces.shoreline) reorient() (in module qsiprep.interfaces.images) reorient_array() (in module qsiprep.interfaces.qc) reorient_tensor_image() (in module qsiprep.interfaces.gradients) reorient_to() (in module qsiprep.interfaces.images) reports_only (qsiprep.config.execution attribute), [1], [2] resource_monitor (qsiprep.config.nipype attribute), [1], [2] RobustMNINormalizationRPT (class in qsiprep.interfaces.niworkflows) rtop_pdf() (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit method) rtop_signal() (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit method) run() (qsiprep.interfaces.tortoise.TORTOISECommandLine method) run_imagemath() (in module qsiprep.interfaces.nilearn) run_uuid (qsiprep.config.execution attribute), [1], [2]

S

safe_get_3d_image() (in module qsiprep.interfaces.epi_fmap) sampling_matrix() (qsiprep.utils.shm.SphHarmModel method) scaled_mip() (in module qsiprep.interfaces.shoreline) scan_groups_to_sidecar() (in module qsiprep.utils.bids) seeds (class in qsiprep.config) select_markers_for_rw() (in module qsiprep.interfaces.nilearn) sentry_setup() (in module qsiprep.utils.sentry) separate_all_dwis (qsiprep.config.workflow attribute), [1], [2] SeriesPreprocReport (class in qsiprep.interfaces.denoise) SeriesQC (class in qsiprep.interfaces.reports) session_id (qsiprep.config.execution attribute), [1], [2] setup_exceptionhook() (in module qsiprep.utils.debug) sf_to_sh() (in module qsiprep.utils.shm) sh_to_rh() (in module qsiprep.utils.shm) sh_to_sf() (in module qsiprep.utils.shm) sh_to_sf_matrix() (in module qsiprep.utils.shm) shape (qsiprep.utils.shm.SphHarmFit property) shm_coeff (qsiprep.utils.shm.SphHarmFit property) shore_coeff (qsiprep.utils.brainsuite_shore.BrainSuiteShoreFit property) shore_index_matrix() (in module qsiprep.utils.brainsuite_shore) shore_matrix_odf() (in module qsiprep.utils.brainsuite_shore) shore_matrix_pdf() (in module qsiprep.utils.brainsuite_shore) shoreline_iters (qsiprep.config.workflow attribute), [1], [2] SHORELineReport (class in qsiprep.interfaces.shoreline) siemens2rads() (in module qsiprep.workflows.fieldmap.utils) SignalPrediction (class in qsiprep.interfaces.shoreline) skip_anat_based_spatial_normalization (qsiprep.config.execution attribute), [1], [2]

SliceQC (class in qsiprep.interfaces.gradients) sloppy (qsiprep.config.execution attribute), [1], [2] smooth_pinv() (in module qsiprep.utils.shm) sph_harm_ind_list() (in module qsiprep.utils.shm) spherical_harmonics() (in module qsiprep.utils.shm) SphHarmFit (class in qsiprep.utils.shm) SphHarmModel (class in qsiprep.utils.shm) split_bvals_bvecs() (in module qsiprep.interfaces.images) split_by_phase_encoding_direction() (in module qsiprep.utils.grouping) split_into_b0s_and_origins() (in module qsiprep.interfaces.epi_fmap) split_into_up_and_down_niis() (in module qsiprep.interfaces.tortoise) SplitDWIsBvals (class in qsiprep.interfaces.images) SplitDWIsFSL (class in qsiprep.interfaces.images) SplitResampledDWIs (class in qsiprep.interfaces.dwi_merge) square_and_normalize_slice() (in module qsiprep.interfaces.qc) StackConfounds (class in qsiprep.interfaces.dwi_merge) start_ping() (in module qsiprep.utils.sentry) stop_on_first_crash (qsiprep.config.nipype attribute), [1], [2] StructuralReference (class in qsiprep.interfaces) (class in qsiprep.interfaces.freesurfer) subject_anatomical_reference (qsiprep.config.workflow attribute), [1], [2] SubjectSummary (class in qsiprep.interfaces) (class in qsiprep.interfaces.reports) subset_bvals() (in module qsiprep.interfaces.dwi_merge) subset_bvecs() (in module qsiprep.interfaces.dwi_merge) SummaryInterface (class in qsiprep.interfaces.reports) SynthSeg (class in qsiprep.interfaces.freesurfer) SynthStrip (class in qsiprep.interfaces.freesurfer)

T

tbspl_eval() (in module qsiprep.utils.bspline) templateflow_home (qsiprep.config.execution attribute), [1], [2] templateflow_version (qsiprep.config.environment attribute), [1], [2] TestInput (class in qsiprep.interfaces.utils) ThreshAndBin (class in qsiprep.workflows.fieldmap.syn), [1] to_filename() (in module qsiprep.config), [1] to_image() (in module qsiprep.interfaces.shoreline) to_lps() (in module qsiprep.interfaces.images)

topup_boilerplate() (in module qsiprep.interfaces.eddy) topup_inputs_from_4d_file() (in module qsiprep.interfaces.fmap) topup_selection_to_report() (in module qsiprep.interfaces.reports) TopupSummary (class in qsiprep.interfaces.reports) TORTOISECommandLine (class in qsiprep.interfaces.tortoise) TORTOISEConvert (class in qsiprep.interfaces.tortoise) TransformHeader (class in qsiprep.interfaces.mrtrix) TSplit (class in qsiprep.interfaces.images)

U

unit_vector() (in module qsiprep.interfaces.dwi_merge) unringing_method (qsiprep.config.workflow attribute), [1], [2]

update_metadata_from_nifti_header() (in module qsiprep.utils.bids) use_syn_sdc (qsiprep.config.workflow attribute), [1], [2] utils (qsiprep.config.loggers attribute), [1], [2]

V

validate_eddy_config() (in module qsiprep.utils.misc) validate_input_dir() (in module qsiprep.utils.bids) ValidateImage (class in qsiprep.interfaces) (class in qsiprep.interfaces.images)

version (qsiprep.config.environment attribute), [1], [2] VoxelSizeChooser (class in qsiprep.interfaces.anatomical)

W

watershed_refined_b0_mask() (in module qsiprep.interfaces.nilearn) work_dir (qsiprep.config.execution attribute), [1], [2] workflow (class in qsiprep.config), [1], [2] (qsiprep.config.loggers attribute), [1], [2]

write_bidsignore() (in module qsiprep.utils.bids) write_concatenated_fsl_gradients() (in module qsiprep.interfaces.gradients) write_derivative_description() (in module qsiprep.utils.bids) write_dummy_bmtxt() (in module qsiprep.interfaces.tortoise) write_graph (qsiprep.config.execution attribute), [1], [2]