Index

_

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

A

AboutSummary (class in qsirecon.interfaces.reports) aggregate_reports() (in module qsirecon.cli.group_report) AggregateAutoTrackResults (class in qsirecon.interfaces.dsi_studio) alpha (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit property) amico_directions_to_fibgz() (in module qsirecon.interfaces.converters) AmicoReconInterface (class in qsirecon.interfaces.amico) AMICOReconScalars (class in qsirecon.interfaces.recon_scalars)

amplitudes_to_fibgz() (in module qsirecon.interfaces.converters) amplitudes_to_sh_mif() (in module qsirecon.interfaces.converters) assert_circular() (qsirecon.utils.testing.TestWorkflow method) assert_inputs_set() (qsirecon.utils.testing.TestWorkflow method) assertIsAlmostExpectedWorkflow() (qsirecon.utils.testing.TestWorkflow method) assertIsSubsetOfList() (qsirecon.utils.testing.TestWorkflow method) AutoTrack (class in qsirecon.interfaces.dsi_studio)

B

before_send() (in module qsirecon.utils.sentry) bids_response_function_to_mrtrix() (in module qsirecon.utils.misc) BIDSError BIDSWarning BrainSuite3dSHOREReconScalars (class in qsirecon.interfaces.recon_scalars) brainsuite_shore_basis() (in module qsirecon.utils.brainsuite_shore) brainsuite_shore_matrix_pdf() (in module qsirecon.utils.brainsuite_shore) BrainSuiteShoreFit (class in qsirecon.utils.brainsuite_shore)

BrainSuiteShoreModel (class in qsirecon.utils.brainsuite_shore) BrainSuiteShoreReconstruction (class in qsirecon.interfaces.dipy) btable_from_bvals_bvecs() (in module qsirecon.interfaces.dsi_studio) build_boilerplate() (in module qsirecon.cli.workflow) build_documentation() (in module qsirecon.utils.boilerplate) build_workflow() (in module qsirecon.cli.workflow) BuildConnectome (class in qsirecon.interfaces.mrtrix) BundleMapper (class in qsirecon.interfaces.scalar_mapping) bvec_to_rasb() (in module qsirecon.interfaces.images)

C

calculate_mask_stats() (in module qsirecon.interfaces.scalar_mapping) calculate_steinhardt() (in module qsirecon.interfaces.anatomical) CalculateSOP (class in qsirecon.interfaces.anatomical) check_deps() (in module qsirecon.utils) (in module qsirecon.utils.misc) check_hsv_inputs() (in module qsirecon.workflows.recon.anatomical) check_latest() (in module qsirecon.cli.version) ChenAutoTrack (class in qsirecon.interfaces.dsi_studio) clean_datasinks() (in module qsirecon.utils.bids) CLIReconPeaksReport (class in qsirecon.interfaces.reports) cnr (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit property) collect_anatomical_data() (in module qsirecon.utils.bids) collect_atlases() (in module qsirecon.utils.atlases) collect_participants() (in module qsirecon.utils.bids) combine_gqi_and_csd_fib_files() (in module qsirecon.interfaces.converters) CompressConnectome2Tck (class in qsirecon.interfaces.mrtrix) ComputeADMap (class in qsirecon.interfaces.tortoise) ComputeFAMap (class in qsirecon.interfaces.tortoise) ComputeLIMap (class in qsirecon.interfaces.tortoise)

ComputeMAPMRI_NG (class in qsirecon.interfaces.tortoise) ComputeMAPMRI_PA (class in qsirecon.interfaces.tortoise) ComputeMAPMRI_RTOP (class in qsirecon.interfaces.tortoise) ComputeMDMap (class in qsirecon.interfaces.tortoise) ComputeRDMap (class in qsirecon.interfaces.tortoise) concatenate_bvals() (in module qsirecon.interfaces.gradients) concatenate_bvecs() (in module qsirecon.interfaces.gradients) ConditionalDoc (class in qsirecon.utils.boilerplate) ConformAtlas (class in qsirecon.interfaces.utils) ConformDwi (class in qsirecon.interfaces) (class in qsirecon.interfaces.images) ConnectivityReport (class in qsirecon.interfaces.reports) Connectome2Tck (class in qsirecon.interfaces.mrtrix) ConvertTransformFile (class in qsirecon.interfaces.ants) copy_boilerplate() (in module qsirecon.cli.workflow) CopyAtlas (class in qsirecon.interfaces.bids) create_rspace() (in module qsirecon.utils.brainsuite_shore) create_sprite_from_tiles() (in module qsirecon.interfaces.qc) createB0_ColorFA_Mask_Sprites() (in module qsirecon.interfaces.qc) createSprite4D() (in module qsirecon.interfaces.qc)

D

deep_update_dict() (in module qsirecon.utils.misc) DerivativesDataSink (class in qsirecon.interfaces) (class in qsirecon.interfaces.bids) describe_atlases() (in module qsirecon.utils.boilerplate) DIPYDKIReconScalars (class in qsirecon.interfaces.recon_scalars) DIPYMAPMRIReconScalars (class in qsirecon.interfaces.recon_scalars) DipyReconInterface (class in qsirecon.interfaces.dipy) DisorganizeScalarData (class in qsirecon.interfaces.recon_scalars) DSIStudioAtlasGraph (class in qsirecon.interfaces.dsi_studio)

DSIStudioConnectivityMatrix (class in qsirecon.interfaces.dsi_studio) DSIStudioCreateSrc (class in qsirecon.interfaces.dsi_studio) DSIStudioExport (class in qsirecon.interfaces.dsi_studio) DSIStudioGQIReconstruction (class in qsirecon.interfaces.dsi_studio) DSIStudioReconScalars (class in qsirecon.interfaces.recon_scalars) DSIStudioReconstruction (class in qsirecon.interfaces.dsi_studio) DSIStudioTracking (class in qsirecon.interfaces.dsi_studio) DSIStudioTrkToTck (class in qsirecon.interfaces.converters) Dwi2Response (class in qsirecon.interfaces.mrtrix)

E

embed_tiles_in_json_sprite() (in module qsirecon.interfaces.qc) EstimateFOD (class in qsirecon.interfaces.mrtrix) EstimateMAPMRI (class in qsirecon.interfaces.tortoise)

EstimateTensor (class in qsirecon.interfaces.tortoise) external_format_datasinks() (in module qsirecon.workflows.recon.dipy) ExtractAtlasFiles (class in qsirecon.interfaces.utils) ExtractB0s (class in qsirecon.interfaces.gradients)

F

fast_load_fibgz() (in module qsirecon.interfaces.converters) fib2amps() (in module qsirecon.interfaces.converters) fib_to_mif() (in module qsirecon.cli.convertODFs) FIBGZtoFOD (class in qsirecon.interfaces.converters)

find_fs_path() (in module qsirecon.interfaces.freesurfer) fit() (qsirecon.utils.brainsuite_shore.BrainSuiteShoreModel method) fitted_signal() (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit method) FixDSIStudioExportHeader (class in qsirecon.interfaces.dsi_studio) FODtoFIBGZ (class in qsirecon.interfaces.converters)

G

GenerateMasked5tt (class in qsirecon.interfaces.mrtrix) get_bids_params() (in module qsirecon.interfaces.bids) get_camera_for_roi() (in module qsirecon.cli.recon_plot) get_doc() (qsirecon.utils.boilerplate.ConditionalDoc method) get_dsi_studio_ODF_geometry() (in module qsirecon.interfaces.converters) get_entity() (in module qsirecon.interfaces.bids) (in module qsirecon.utils.bids)

get_inputs_outputs() (qsirecon.utils.testing.TestWorkflow method) get_iterable_dwis_and_anats() (in module qsirecon.utils.bids) get_l_m() (in module qsirecon.interfaces.anatomical) get_middle_slice_tiles() (in module qsirecon.interfaces.qc) get_recon_output_name() (in module qsirecon.interfaces.bids) GetTemplate (class in qsirecon.interfaces.anatomical) GlobalTractography (class in qsirecon.interfaces.mrtrix) GradientSelect (class in qsirecon.interfaces.gradients)

I

ImageMath (class in qsirecon.interfaces.ants) infer_deltas() (in module qsirecon.workflows.recon.dipy) init_amico_noddi_fit_wf() (in module qsirecon.workflows.recon.amico) init_conform_dwi_wf() (in module qsirecon.workflows.recon.utils) init_dipy_brainsuite_shore_recon_wf() (in module qsirecon.workflows.recon.dipy) init_dipy_dki_recon_wf() (in module qsirecon.workflows.recon.dipy) init_dipy_mapmri_recon_wf() (in module qsirecon.workflows.recon.dipy) init_discard_repeated_samples_wf() (in module qsirecon.workflows.recon.utils) init_dsi_studio_autotrack_registration_wf() (in module qsirecon.workflows.recon.dsi_studio) init_dsi_studio_autotrack_wf() (in module qsirecon.workflows.recon.dsi_studio) init_dsi_studio_connectivity_wf() (in module qsirecon.workflows.recon.dsi_studio) init_dsi_studio_export_wf() (in module qsirecon.workflows.recon.dsi_studio) init_dsi_studio_recon_wf() (in module qsirecon.workflows.recon.dsi_studio) init_dsi_studio_tractography_wf() (in module qsirecon.workflows.recon.dsi_studio) init_dwi_recon_anatomical_workflow() (in module qsirecon.workflows.recon.anatomical) init_dwi_recon_workflow() (in module qsirecon.workflows.recon.build_workflow) init_fibgz_to_mif_wf() (in module qsirecon.workflows.recon.converters) init_fod_fib_wf() (in module qsirecon.workflows.recon.converters) init_global_tractography_wf() (in module qsirecon.workflows.recon.mrtrix) init_gradient_select_wf() (in module qsirecon.workflows.recon.utils) init_highres_recon_anatomical_wf() (in module qsirecon.workflows.recon.anatomical) init_json_preproc_report_wf() (in module qsirecon.workflows.reports)

init_mif_to_fibgz_wf() (in module qsirecon.workflows.recon.converters) init_mrtrix_connectivity_wf() (in module qsirecon.workflows.recon.mrtrix) init_mrtrix_csd_recon_wf() (in module qsirecon.workflows.recon.mrtrix) init_mrtrix_tractography_wf() (in module qsirecon.workflows.recon.mrtrix) init_output_grid_wf() (in module qsirecon.workflows.recon.anatomical) init_pyafq_wf() (in module qsirecon.workflows.recon.pyafq) init_qsirecon_to_fsl_wf() (in module qsirecon.workflows.recon.converters) init_qsirecon_wf() (in module qsirecon.workflows.base) init_register_fs_to_qsiprep_wf() (in module qsirecon.workflows.recon.anatomical) init_scalar_output_wf() (in module qsirecon.workflows.recon.utils) init_scalar_to_atlas_wf() (in module qsirecon.workflows.recon.scalar_mapping) init_scalar_to_bundle_wf() (in module qsirecon.workflows.recon.scalar_mapping) init_scalar_to_surface_wf() (in module qsirecon.workflows.recon.scalar_mapping) init_scalar_to_template_wf() (in module qsirecon.workflows.recon.scalar_mapping) init_single_subject_json_report_wf() (in module qsirecon.workflows.reports) init_single_subject_recon_wf() (in module qsirecon.workflows.base) init_steinhardt_order_param_wf() (in module qsirecon.workflows.recon.steinhardt) init_test_wf() (in module qsirecon.workflows.recon.utils) init_tortoise_estimator_wf() (in module qsirecon.workflows.recon.tortoise) InteractiveReport (class in qsirecon.interfaces.reports) is_flagged() (in module qsirecon.cli.version) is_interactive() (in module qsirecon.utils.debug) ITKTransformConvert (class in qsirecon.interfaces.mrtrix)

K

KurtosisReconstruction (class in qsirecon.interfaces.dipy)

KurtosisReconstructionMicrostructure (class in qsirecon.interfaces.dipy) KurtosisReconstructionMSDKI (class in qsirecon.interfaces.dipy)

L

label_convert() (in module qsirecon.interfaces.utils) list_to_str() (in module qsirecon.utils.boilerplate) listify() (in module qsirecon.utils.misc)

load_and_reorient() (in module qsirecon.interfaces.qc) load_yaml() (in module qsirecon.utils.misc) LoadResponseFunctions (class in qsirecon.interfaces.utils)

M

main() (in module qsirecon.cli.run) make_a_square() (in module qsirecon.interfaces.qc) make_bmat_file() (in module qsirecon.interfaces.tortoise) make_sloppy() (in module qsirecon.utils.sloppy_recon) MAPMRIReconstruction (class in qsirecon.interfaces.dipy) MergeFODGQIFibs (class in qsirecon.interfaces.converters) mif2amps() (in module qsirecon.interfaces.converters) mif_to_fib() (in module qsirecon.cli.convertODFs) module qsirecon qsirecon.cli qsirecon.cli.convertODFs qsirecon.cli.group_report qsirecon.cli.parser qsirecon.cli.recon_plot qsirecon.cli.run qsirecon.cli.version qsirecon.cli.workflow qsirecon.interfaces qsirecon.interfaces.amico qsirecon.interfaces.anatomical qsirecon.interfaces.ants qsirecon.interfaces.bids qsirecon.interfaces.converters qsirecon.interfaces.denoise qsirecon.interfaces.dipy qsirecon.interfaces.dsi_studio qsirecon.interfaces.freesurfer qsirecon.interfaces.gradients qsirecon.interfaces.images qsirecon.interfaces.ingress qsirecon.interfaces.interchange qsirecon.interfaces.mrtrix qsirecon.interfaces.pyafq qsirecon.interfaces.qc qsirecon.interfaces.recon_scalars qsirecon.interfaces.reports qsirecon.interfaces.scalar_mapping qsirecon.interfaces.tortoise qsirecon.interfaces.utils qsirecon.utils qsirecon.utils.atlases qsirecon.utils.bids qsirecon.utils.boilerplate qsirecon.utils.brainsuite_shore qsirecon.utils.debug qsirecon.utils.maths qsirecon.utils.misc qsirecon.utils.sentry qsirecon.utils.sloppy_recon qsirecon.utils.testing qsirecon.workflows qsirecon.workflows.base qsirecon.workflows.recon qsirecon.workflows.recon.amico qsirecon.workflows.recon.anatomical qsirecon.workflows.recon.build_workflow qsirecon.workflows.recon.converters qsirecon.workflows.recon.dipy qsirecon.workflows.recon.dsi_studio qsirecon.workflows.recon.mrtrix qsirecon.workflows.recon.pyafq qsirecon.workflows.recon.scalar_mapping qsirecon.workflows.recon.steinhardt qsirecon.workflows.recon.tortoise qsirecon.workflows.recon.utils qsirecon.workflows.reports

mplfig() (in module qsirecon.interfaces.qc) mplfigcontour() (in module qsirecon.interfaces.qc) mrtrix_response_function_to_bids() (in module qsirecon.utils.misc) MRTrixAtlasGraph (class in qsirecon.interfaces.mrtrix) MRTrixGradientTable (class in qsirecon.interfaces.mrtrix) MRTrixIngress (class in qsirecon.interfaces.mrtrix) msd() (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit method) MTNormalize (class in qsirecon.interfaces.mrtrix)

N

nearest_square() (in module qsirecon.interfaces.qc) NODDI (class in qsirecon.interfaces.amico)

NODDITissueFraction (class in qsirecon.interfaces.amico) NODDItoFIBGZ (class in qsirecon.interfaces.converters)

O

odf() (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit method) odf_roi_plot() (in module qsirecon.cli.recon_plot) odf_sh() (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit method)

OrganizeScalarData (class in qsirecon.interfaces.recon_scalars) out_path_base (qsirecon.interfaces.bids.DerivativesDataSink attribute) (qsirecon.interfaces.bids.ReconDerivativesDataSink attribute) (qsirecon.interfaces.DerivativesDataSink attribute)

P

ParcellateScalars (class in qsirecon.interfaces.recon_scalars) ParcellationTableSplitterDataSink (class in qsirecon.interfaces.recon_scalars) parse_args() (in module qsirecon.cli.parser) pdf() (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit method) pdf_grid() (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit method) peak_slice_series() (in module qsirecon.cli.recon_plot) peaks_from_odfs() (in module qsirecon.cli.recon_plot)

peaks_to_odfs() (in module qsirecon.interfaces.converters) plot_an_odf_slice() (in module qsirecon.cli.recon_plot) plot_peak_slice() (in module qsirecon.cli.recon_plot) plot_scalar_map() (in module qsirecon.interfaces.reports) popen_run() (in module qsirecon.interfaces.converters) predict() (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit method) process_crashfile() (in module qsirecon.utils.sentry) PyAFQRecon (class in qsirecon.interfaces.pyafq)

Q

QSIPrepAnatomicalIngress (class in qsirecon.interfaces.anatomical) QSIPrepDWIIngress (class in qsirecon.interfaces.ingress) qsirecon module qsirecon.cli module qsirecon.cli.convertODFs module qsirecon.cli.group_report module qsirecon.cli.parser module qsirecon.cli.recon_plot module qsirecon.cli.run module qsirecon.cli.version module qsirecon.cli.workflow module qsirecon.interfaces module qsirecon.interfaces.amico module qsirecon.interfaces.anatomical module qsirecon.interfaces.ants module qsirecon.interfaces.bids module qsirecon.interfaces.converters module qsirecon.interfaces.denoise module qsirecon.interfaces.dipy module qsirecon.interfaces.dsi_studio module qsirecon.interfaces.freesurfer module qsirecon.interfaces.gradients module qsirecon.interfaces.images module qsirecon.interfaces.ingress module qsirecon.interfaces.interchange module qsirecon.interfaces.mrtrix module qsirecon.interfaces.pyafq module qsirecon.interfaces.qc module qsirecon.interfaces.recon_scalars module qsirecon.interfaces.reports module qsirecon.interfaces.scalar_mapping module

qsirecon.interfaces.tortoise module qsirecon.interfaces.utils module qsirecon.utils module qsirecon.utils.atlases module qsirecon.utils.bids module qsirecon.utils.boilerplate module qsirecon.utils.brainsuite_shore module qsirecon.utils.debug module qsirecon.utils.maths module qsirecon.utils.misc module qsirecon.utils.sentry module qsirecon.utils.sloppy_recon module qsirecon.utils.testing module qsirecon.workflows module qsirecon.workflows.base module qsirecon.workflows.recon module qsirecon.workflows.recon.amico module qsirecon.workflows.recon.anatomical module qsirecon.workflows.recon.build_workflow module qsirecon.workflows.recon.converters module qsirecon.workflows.recon.dipy module qsirecon.workflows.recon.dsi_studio module qsirecon.workflows.recon.mrtrix module qsirecon.workflows.recon.pyafq module qsirecon.workflows.recon.scalar_mapping module qsirecon.workflows.recon.steinhardt module qsirecon.workflows.recon.tortoise module qsirecon.workflows.recon.utils module qsirecon.workflows.reports module

R

r2 (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit property) RecombineAtlasConfigs (class in qsirecon.interfaces.utils) recon_plot() (in module qsirecon.cli.recon_plot) ReconAnatomicalData (class in qsirecon.interfaces.interchange) ReconDerivativesDataSink (class in qsirecon.interfaces.bids) ReconScalars (class in qsirecon.interfaces.recon_scalars) ReconScalarsTableSplitterDataSink (class in qsirecon.interfaces.recon_scalars)

ReconWorkflowInputs (class in qsirecon.interfaces.interchange) regularization (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit property) remove_non_alphanumeric() (in module qsirecon.utils.misc) RemoveDuplicates (class in qsirecon.interfaces.gradients) reorient_array() (in module qsirecon.interfaces.qc) rtop_pdf() (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit method) rtop_signal() (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit method) run() (qsirecon.interfaces.tortoise.TORTOISECommandLine method)

S

scalar_metadata (qsirecon.interfaces.recon_scalars.AMICOReconScalars attribute) (qsirecon.interfaces.recon_scalars.BrainSuite3dSHOREReconScalars attribute) (qsirecon.interfaces.recon_scalars.DIPYDKIReconScalars attribute) (qsirecon.interfaces.recon_scalars.DIPYMAPMRIReconScalars attribute) (qsirecon.interfaces.recon_scalars.DSIStudioReconScalars attribute) (qsirecon.interfaces.recon_scalars.ReconScalars attribute) (qsirecon.interfaces.recon_scalars.TORTOISEReconScalars attribute) ScalarMapper (class in qsirecon.interfaces.scalar_mapping) ScalarReport (class in qsirecon.interfaces.reports) sentry_setup() (in module qsirecon.utils.sentry) SeriesPreprocReport (class in qsirecon.interfaces.denoise) setup_exceptionhook() (in module qsirecon.utils.debug) shore_coeff (qsirecon.utils.brainsuite_shore.BrainSuiteShoreFit property) shore_index_matrix() (in module qsirecon.utils.brainsuite_shore)

shore_matrix_odf() (in module qsirecon.utils.brainsuite_shore) shore_matrix_pdf() (in module qsirecon.utils.brainsuite_shore) SIFT2 (class in qsirecon.interfaces.mrtrix) sink_mask_file() (in module qsirecon.cli.convertODFs) (in module qsirecon.cli.recon_plot) SplitAtlasConfigs (class in qsirecon.interfaces.utils) square_and_normalize_slice() (in module qsirecon.interfaces.qc) SS3TBase (class in qsirecon.interfaces.mrtrix) SS3TDwi2Response (class in qsirecon.interfaces.mrtrix) SS3TEstimateFOD (class in qsirecon.interfaces.mrtrix) start_ping() (in module qsirecon.utils.sentry) stat_txt_to_df() (in module qsirecon.interfaces.dsi_studio) SubjectSummary (class in qsirecon.interfaces.reports) subset_dwi() (in module qsirecon.interfaces.gradients) SummaryInterface (class in qsirecon.interfaces.reports)

T

TckGen (class in qsirecon.interfaces.mrtrix) TemplateMapper (class in qsirecon.interfaces.scalar_mapping) TensorReconstruction (class in qsirecon.interfaces.dipy) TestReportPlot (class in qsirecon.interfaces.utils) TestWorkflow (class in qsirecon.utils.testing) to_lps() (in module qsirecon.interfaces.images)

ToDict (class in qsirecon.cli.parser) TORTOISECommandLine (class in qsirecon.interfaces.tortoise) TORTOISEConvert (class in qsirecon.interfaces.tortoise) TORTOISEReconCommandLine (class in qsirecon.interfaces.tortoise) TORTOISEReconScalars (class in qsirecon.interfaces.recon_scalars) TransformHeader (class in qsirecon.interfaces.mrtrix)

U

update_params() (in module qsirecon.utils.sloppy_recon)

V

validate_input_dir() (in module qsirecon.utils.bids) ValidateImage (class in qsirecon.interfaces) (class in qsirecon.interfaces.images)

VoxelSizeChooser (class in qsirecon.interfaces.anatomical)

W

WarpConnectivityAtlases (class in qsirecon.interfaces.utils) workflow_from_spec() (in module qsirecon.workflows.recon.build_workflow) write_atlas_dataset_description() (in module qsirecon.utils.bids)

write_bidsignore() (in module qsirecon.utils.bids) write_derivative_description() (in module qsirecon.utils.bids) WriteSidecar (class in qsirecon.interfaces.utils)