Index

Symbols

--acqp_file <acqp_file> dmriprep command line option --b0_thresh <b0_thresh> dmriprep command line option --bet_dwi <bet_dwi> dmriprep command line option --bet_mag <bet_mag> dmriprep command line option --concat_dwis <concat_dwis> dmriprep command line option --ignore <ignore> dmriprep command line option --n_cpus <nthreads> dmriprep command line option --nthreads dmriprep command line option --omp_nthreads <omp_nthreads> dmriprep command line option --output_resolution <output_resolution> dmriprep command line option --participant_label <participant_label> dmriprep command line option

--session_label <session_label> dmriprep command line option --skip_bids_validation dmriprep command line option --slspec_file <slspec_file> dmriprep command line option --synb0_dir <synb0_dir> dmriprep command line option --use_ants dmriprep command line option --use_brainsuite dmriprep command line option --work_dir <work_dir> dmriprep command line option --write_graph dmriprep command line option -i dmriprep command line option -w dmriprep command line option

A

activate() (dmriprep.due.InactiveDueCreditCollector method) active (dmriprep.due.InactiveDueCreditCollector attribute)

add() (dmriprep.due.InactiveDueCreditCollector method) ANALYSIS_LEVEL dmriprep command line option

B

BibTeX() (in module dmriprep.due) BIDS_DIR dmriprep command line option

BIDSError BIDSWarning

C

cite() (dmriprep.due.InactiveDueCreditCollector method) collect_data() (in module dmriprep.utils.bids) collect_participants() (in module dmriprep.utils.bids) coolwarm_transparent() (in module dmriprep.viz.utils) create_report_json() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc)

create_sprite_from_tiles() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc) createB0_ColorFA_Mask_Sprites() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc) createSprite4D() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc)

D

dcite() (dmriprep.due.InactiveDueCreditCollector method) delta_te() (in module dmriprep.workflows.fieldmap.phasediff) dmriprep (module) dmriprep command line option --acqp_file <acqp_file> --b0_thresh <b0_thresh> --bet_dwi <bet_dwi> --bet_mag <bet_mag> --concat_dwis <concat_dwis> --ignore <ignore> --n_cpus <nthreads> --nthreads --omp_nthreads <omp_nthreads> --output_resolution <output_resolution> --participant_label <participant_label> --session_label <session_label> --skip_bids_validation --slspec_file <slspec_file> --synb0_dir <synb0_dir> --use_ants --use_brainsuite --work_dir <work_dir> --write_graph -i -w ANALYSIS_LEVEL BIDS_DIR OUTPUT_DIR dmriprep.cli (module)

dmriprep.due (module) dmriprep.interfaces (module) dmriprep.interfaces.fmap (module) dmriprep.interfaces.reportlets (module) dmriprep.qc (module) dmriprep.utils (module) dmriprep.utils.bids (module) dmriprep.utils.hemisphere (module) dmriprep.viz (module) dmriprep.viz.utils (module) dmriprep.workflows (module) dmriprep.workflows.anatomical (module) dmriprep.workflows.base (module) dmriprep.workflows.dwi (module) dmriprep.workflows.dwi.artifacts (module), [1] dmriprep.workflows.dwi.base (module), [1] dmriprep.workflows.dwi.eddy (module), [1] dmriprep.workflows.dwi.outputs (module), [1] dmriprep.workflows.dwi.qc (module) dmriprep.workflows.dwi.tensor (module), [1] dmriprep.workflows.dwi.util (module), [1] dmriprep.workflows.fieldmap (module) dmriprep.workflows.fieldmap.base (module) dmriprep.workflows.fieldmap.brainsuite (module) dmriprep.workflows.fieldmap.fmap (module) dmriprep.workflows.fieldmap.pepolar (module) dmriprep.workflows.fieldmap.phasediff (module) dmriprep.workflows.fieldmap.synb0 (module) Doi() (in module dmriprep.due) dump() (dmriprep.due.InactiveDueCreditCollector method)

F

FieldEnhance (class in dmriprep.interfaces.fmap) FieldEnhanceInputSpec (class in dmriprep.interfaces.fmap) FieldEnhanceOutputSpec (class in dmriprep.interfaces.fmap) FieldmapReportlet (class in dmriprep.interfaces.reportlets) FieldmapReportletInputSpec (class in dmriprep.interfaces.reportlets)

FieldToHz (class in dmriprep.interfaces.fmap) FieldToHzInputSpec (class in dmriprep.interfaces.fmap) FieldToHzOutputSpec (class in dmriprep.interfaces.fmap) FieldToRadS (class in dmriprep.interfaces.fmap) FieldToRadSInputSpec (class in dmriprep.interfaces.fmap) FieldToRadSOutputSpec (class in dmriprep.interfaces.fmap)

G

get_ees() (in module dmriprep.interfaces.fmap) get_middle_slices() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc)

get_trt() (in module dmriprep.interfaces.fmap) group_dwi() (in module dmriprep.utils.bids)

I

InactiveDueCreditCollector (class in dmriprep.due) init_anat_preproc_wf() (in module dmriprep.workflows.anatomical), [1] init_brainsuite_wf() (in module dmriprep.workflows.fieldmap.brainsuite), [1] init_dmriprep_wf() (in module dmriprep.workflows.base), [1] init_dwi_artifacts_wf() (in module dmriprep.workflows.dwi) (in module dmriprep.workflows.dwi.artifacts), [1], [2] init_dwi_concat_wf() (in module dmriprep.workflows.dwi) (in module dmriprep.workflows.dwi.util), [1], [2] init_dwi_derivatives_wf() (in module dmriprep.workflows.dwi) (in module dmriprep.workflows.dwi.outputs), [1], [2] init_dwi_eddy_wf() (in module dmriprep.workflows.dwi) (in module dmriprep.workflows.dwi.eddy), [1], [2] init_dwi_preproc_wf() (in module dmriprep.workflows.dwi) (in module dmriprep.workflows.dwi.base), [1], [2] init_dwi_tensor_wf() (in module dmriprep.workflows.dwi) (in module dmriprep.workflows.dwi.tensor), [1], [2]

init_fmap_wf() (in module dmriprep.workflows.fieldmap.fmap) init_pepolar_wf() (in module dmriprep.workflows.fieldmap.pepolar) init_phase_wf() (in module dmriprep.workflows.fieldmap.phasediff) init_phdiff_wf() (in module dmriprep.workflows.fieldmap.phasediff) init_sdc_wf() (in module dmriprep.workflows.fieldmap.base) init_single_subject_wf() (in module dmriprep.workflows.base), [1] init_synb0_wf() (in module dmriprep.workflows.fieldmap.pepolar) init_topup_wf() (in module dmriprep.workflows.fieldmap.pepolar) input_spec (dmriprep.interfaces.fmap.FieldEnhance attribute) (dmriprep.interfaces.fmap.FieldToHz attribute) (dmriprep.interfaces.fmap.FieldToRadS attribute) (dmriprep.interfaces.fmap.Phasediff2Fieldmap attribute) (dmriprep.interfaces.fmap.Phases2Fieldmap attribute) (dmriprep.interfaces.reportlets.FieldmapReportlet attribute) is_hemispherical() (in module dmriprep.utils.hemisphere)

L

load() (dmriprep.due.InactiveDueCreditCollector method)

load_and_reorient() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc)

M

mplfig() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc)

mplfigcontour() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc)

N

nearest_square() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc)

O

OUTPUT_DIR dmriprep command line option output_spec (dmriprep.interfaces.fmap.FieldEnhance attribute) (dmriprep.interfaces.fmap.FieldToHz attribute) (dmriprep.interfaces.fmap.FieldToRadS attribute) (dmriprep.interfaces.fmap.Phasediff2Fieldmap attribute) (dmriprep.interfaces.fmap.Phases2Fieldmap attribute) (dmriprep.interfaces.reportlets.FieldmapReportlet attribute)

P

Phasediff2Fieldmap (class in dmriprep.interfaces.fmap) Phasediff2FieldmapInputSpec (class in dmriprep.interfaces.fmap) Phasediff2FieldmapOutputSpec (class in dmriprep.interfaces.fmap) Phases2Fieldmap (class in dmriprep.interfaces.fmap)

Phases2FieldmapInputSpec (class in dmriprep.interfaces.fmap) Phases2FieldmapOutputSpec (class in dmriprep.interfaces.fmap) phases2fmap() (in module dmriprep.interfaces.fmap) phdiff2fmap() (in module dmriprep.interfaces.fmap) plot_registration() (in module dmriprep.viz.utils)

R

reorient_array() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc) reshape3D() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc)

reshape4D() (in module dmriprep.qc) (in module dmriprep.workflows.dwi.qc)

T

Text() (in module dmriprep.due)

U

Url() (in module dmriprep.due)

V

validate_input_dir() (in module dmriprep.utils.bids)