Index

_

_Config (class in dmriprep.config)

A

AboutSummary (class in dmriprep.interfaces.reports) affine (dmriprep.utils.vectors.DiffusionGradientTable property)

anat_only (dmriprep.config.workflow attribute) ants (dmriprep.config.seeds attribute)

B

b0mask (dmriprep.utils.vectors.DiffusionGradientTable property) bids_database_dir (dmriprep.config.execution attribute) bids_description_hash (dmriprep.config.execution attribute) bids_dir (dmriprep.config.execution attribute) bids_filters (dmriprep.config.execution attribute) BIDSDataGrabber (class in dmriprep.interfaces)

BIDSSourceFile (class in dmriprep.interfaces.bids) BIDSURI (class in dmriprep.interfaces.bids) boilerplate_only (dmriprep.config.execution attribute) bvals (dmriprep.utils.vectors.DiffusionGradientTable property) bvecs (dmriprep.utils.vectors.DiffusionGradientTable property) bvecs2ras() (in module dmriprep.utils.vectors)

C

calculate_pole() (in module dmriprep.utils.vectors) check_deps() (in module dmriprep.utils.misc) CheckGradientTable (class in dmriprep.interfaces.vectors) cifti_output (dmriprep.config.workflow attribute) clean_datasinks() (in module dmriprep.workflows.base)

cli (dmriprep.config.loggers attribute) collect_derivatives() (in module dmriprep.utils.bids) count_shells (dmriprep.utils.vectors.DiffusionGradientTable property) cpu_count (dmriprep.config.environment attribute) crashfile_format (dmriprep.config.nipype attribute) CreateFreeSurferID (class in dmriprep.interfaces.bids)

D

dataset_links (dmriprep.config.execution attribute) debug (dmriprep.config.execution attribute) default (dmriprep.config.loggers attribute) derivatives (dmriprep.config.execution attribute) DerivativesDataSink (class in dmriprep.interfaces) DiffusionGradientTable (class in dmriprep.utils.vectors) DiffusionSummary (class in dmriprep.interfaces.reports) dmriprep.config module dmriprep.interfaces module dmriprep.interfaces.bids module dmriprep.interfaces.images module dmriprep.interfaces.reports module dmriprep.interfaces.vectors module dmriprep.utils module dmriprep.utils.bids module

dmriprep.utils.images module dmriprep.utils.misc module dmriprep.utils.vectors module dmriprep.workflows module dmriprep.workflows.base module dmriprep.workflows.dwi module dmriprep.workflows.dwi.base module dmriprep.workflows.dwi.eddy module dmriprep.workflows.dwi.outputs module dmriprep_dir (dmriprep.config.execution attribute) dumps() (in module dmriprep.config) dwi2anat_dof (dmriprep.config.workflow attribute) dwi2anat_init (dmriprep.config.workflow attribute)

E

environment (class in dmriprep.config) estimate_image_mem_usage() (in module dmriprep.utils.misc) exec_docker_version (dmriprep.config.environment attribute) exec_env (dmriprep.config.environment attribute)

execution (class in dmriprep.config) extract_b0() (in module dmriprep.utils.images) extract_entities() (in module dmriprep.utils.bids) ExtractB0 (class in dmriprep.interfaces.images)

F

fallback_total_readout_time (dmriprep.config.workflow attribute) fips_enabled() (in module dmriprep.utils.misc) fmap_bspline (dmriprep.config.workflow attribute) fmap_demean (dmriprep.config.workflow attribute) fmt_subjects_sessions() (in module dmriprep.utils.misc)

force (dmriprep.config.workflow attribute) free_mem (dmriprep.config.environment attribute) from_dict() (in module dmriprep.config) fs_license_file (dmriprep.config.execution attribute) fs_no_resume (dmriprep.config.workflow attribute) fs_subjects_dir (dmriprep.config.execution attribute)

G

gen_eddy_textfiles() (in module dmriprep.workflows.dwi.eddy) generate_rasb() (dmriprep.utils.vectors.DiffusionGradientTable method) generate_vecval() (dmriprep.utils.vectors.DiffusionGradientTable method) get() (dmriprep.config._Config class method) (in module dmriprep.config)

get_estimator() (in module dmriprep.workflows.base) get_linked_libs (dmriprep.config.nipype attribute) get_list_data() (in module dmriprep.utils.images) get_plugin() (dmriprep.config.nipype class method) gradients (dmriprep.utils.vectors.DiffusionGradientTable property)

H

hires (dmriprep.config.workflow attribute)

I

ignore (dmriprep.config.workflow attribute) init() (dmriprep.config.execution class method) (dmriprep.config.loggers class method) (dmriprep.config.nipype class method) (dmriprep.config.seeds class method) init_dmriprep_wf() (in module dmriprep.workflows.base) init_dwi_derivatives_wf() (in module dmriprep.workflows.dwi.outputs)

init_dwi_wf() (in module dmriprep.workflows.dwi.base) init_eddy_wf() (in module dmriprep.workflows.dwi.eddy) init_reportlets_wf() (in module dmriprep.workflows.dwi.outputs) init_single_subject_wf() (in module dmriprep.workflows.base) init_spaces() (in module dmriprep.config) input_spec (dmriprep.interfaces.bids.BIDSURI attribute) interface (dmriprep.config.loggers attribute)

L

layout (dmriprep.config.execution attribute) level (dmriprep.config.workflow attribute) load() (dmriprep.config._Config class method) (in module dmriprep.config)

log_dir (dmriprep.config.execution attribute) log_level (dmriprep.config.execution attribute) loggers (class in dmriprep.config) low_mem (dmriprep.config.execution attribute)

M

map_fieldmap_estimation() (in module dmriprep.workflows.base) master (dmriprep.config.seeds attribute) match_transforms() (in module dmriprep.utils.images) md_only_boilerplate (dmriprep.config.execution attribute) memory_gb (dmriprep.config.nipype attribute) module dmriprep.config dmriprep.interfaces dmriprep.interfaces.bids dmriprep.interfaces.images dmriprep.interfaces.reports dmriprep.interfaces.vectors dmriprep.utils dmriprep.utils.bids dmriprep.utils.images dmriprep.utils.misc dmriprep.utils.vectors dmriprep.workflows dmriprep.workflows.base dmriprep.workflows.dwi dmriprep.workflows.dwi.base dmriprep.workflows.dwi.eddy dmriprep.workflows.dwi.outputs

N

nipype (class in dmriprep.config) nipype_version (dmriprep.config.environment attribute) normalize() (dmriprep.utils.vectors.DiffusionGradientTable method) normalize_gradients() (in module dmriprep.utils.vectors)

normalized (dmriprep.utils.vectors.DiffusionGradientTable property) notrack (dmriprep.config.execution attribute) nprocs (dmriprep.config.nipype attribute) numpy (dmriprep.config.seeds attribute)

O

omp_nthreads (dmriprep.config.nipype attribute) out_path_base (dmriprep.interfaces.DerivativesDataSink attribute) output_dir (dmriprep.config.execution attribute)

output_layout (dmriprep.config.execution attribute) output_spaces (dmriprep.config.execution attribute) overcommit_limit (dmriprep.config.environment attribute) overcommit_policy (dmriprep.config.environment attribute)

P

parameterize_dirs (dmriprep.config.nipype attribute) participant_label (dmriprep.config.execution attribute) plugin (dmriprep.config.nipype attribute)

plugin_args (dmriprep.config.nipype attribute) pole (dmriprep.utils.vectors.DiffusionGradientTable property) processing_groups (dmriprep.config.execution attribute)

R

rasb_dwi_length_check() (in module dmriprep.utils.vectors) redirect_warnings() (in module dmriprep.config) reorient_rasb() (dmriprep.utils.vectors.DiffusionGradientTable method) reports_only (dmriprep.config.execution attribute) rescale_b0() (in module dmriprep.utils.images)

RescaleB0 (class in dmriprep.interfaces.images) resource_monitor (dmriprep.config.nipype attribute) run_msmsulc (dmriprep.config.workflow attribute) run_reconall (dmriprep.config.workflow attribute) run_uuid (dmriprep.config.execution attribute)

S

save_3d_to_4d() (in module dmriprep.utils.images) save_4d_to_3d() (in module dmriprep.utils.images) seeds (class in dmriprep.config) session_label (dmriprep.config.execution attribute) skull_strip_fixed_seed (dmriprep.config.workflow attribute) skull_strip_t1w (dmriprep.config.workflow attribute) skull_strip_template (dmriprep.config.workflow attribute)

sloppy (dmriprep.config.execution attribute) spaces (dmriprep.config.workflow attribute) stop_on_first_crash (dmriprep.config.nipype attribute) subject_anatomical_reference (dmriprep.config.workflow attribute) SubjectSummary (class in dmriprep.interfaces.reports) summarize_images() (in module dmriprep.utils.images) SummaryInterface (class in dmriprep.interfaces.reports)

T

templateflow_home (dmriprep.config.execution attribute) templateflow_version (dmriprep.config.environment attribute)

to_filename() (dmriprep.utils.vectors.DiffusionGradientTable method) (in module dmriprep.config)

U

use_bbr (dmriprep.config.workflow attribute)

use_syn_sdc (dmriprep.config.workflow attribute) utils (dmriprep.config.loggers attribute)

V

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

version (dmriprep.config.environment attribute)

W

work_dir (dmriprep.config.execution attribute) workflow (class in dmriprep.config) (dmriprep.config.loggers attribute)

write_bidsignore() (in module dmriprep.utils.bids) write_derivative_description() (in module dmriprep.utils.bids) write_graph (dmriprep.config.execution attribute)