Index

Symbols

--bval kwneuro-dwi-denoise command line option kwneuro-dwi-dti command line option kwneuro-dwi-mean-b0 command line option kwneuro-registration-dwi-to-structural command line option --bvec kwneuro-dwi-denoise command line option kwneuro-dwi-dti command line option kwneuro-dwi-mean-b0 command line option kwneuro-registration-dwi-to-structural command line option --dwi kwneuro-dwi-denoise command line option kwneuro-dwi-dti command line option kwneuro-dwi-mean-b0 command line option kwneuro-registration-dwi-to-structural command line option --dwi-mask kwneuro-registration-dwi-to-structural command line option --fixed kwneuro-registration-apply command line option kwneuro-registration-volumes command line option --image kwneuro-structural-bias-correct command line option kwneuro-structural-extract-brain command line option kwneuro-structural-parcellate command line option kwneuro-structural-segment-tissues command line option --inputs kwneuro-mask-dwi-batch command line option kwneuro-mask-structural-batch command line option --interpolation kwneuro-registration-apply command line option --invert kwneuro-registration-apply command line option --mask kwneuro-dwi-dti command line option kwneuro-registration-volumes command line option kwneuro-structural-segment-tissues command line option --method kwneuro-structural-parcellate command line option kwneuro-structural-segment-tissues command line option

--moving kwneuro-registration-apply command line option kwneuro-registration-volumes command line option --moving-mask kwneuro-registration-volumes command line option --out kwneuro-dwi-mean-b0 command line option kwneuro-registration-apply command line option kwneuro-registration-volumes command line option kwneuro-structural-bias-correct command line option kwneuro-structural-parcellate command line option kwneuro-structural-segment-tissues command line option --out-dti kwneuro-dwi-dti command line option --out-dwi kwneuro-dwi-denoise command line option --out-fa kwneuro-dwi-dti command line option --out-mask kwneuro-structural-extract-brain command line option --out-md kwneuro-dwi-dti command line option --out-transform kwneuro-registration-dwi-to-structural command line option kwneuro-registration-volumes command line option --outputs kwneuro-mask-dwi-batch command line option kwneuro-mask-structural-batch command line option --sequential kwneuro-mask-dwi-batch command line option kwneuro-mask-structural-batch command line option --structural kwneuro-registration-dwi-to-structural command line option --structural-mask kwneuro-registration-dwi-to-structural command line option --transform kwneuro-registration-apply command line option kwneuro-registration-dwi-to-structural command line option kwneuro-registration-volumes command line option

A

affine (kwneuro.resource.InMemoryVolumeResource attribute) apply() (kwneuro.reg.TransformResource method) array (kwneuro.resource.InMemoryBvalResource attribute) (kwneuro.resource.InMemoryBvecResource attribute) (kwneuro.resource.InMemoryVolumeResource attribute)

average_volumes() (in module kwneuro.build_template) avg_signal (kwneuro.resource.InMemoryResponseFunctionResource attribute)

B

brain_extract() (in module kwneuro.masks) brain_extract_dwi_batch() (in module kwneuro.masks) brain_extract_structural_batch() (in module kwneuro.masks) build_multi_metric_template() (in module kwneuro.build_template) build_template() (in module kwneuro.build_template) bval (kwneuro.Dwi attribute) (kwneuro.dwi.Dwi attribute) (kwneuro.external.TemporaryDwiFiles attribute)

BvalResource (class in kwneuro.resource) bvec (kwneuro.Dwi attribute) (kwneuro.dwi.Dwi attribute) (kwneuro.external.TemporaryDwiFiles attribute) BvecResource (class in kwneuro.resource)

C

Cache (class in kwneuro) (class in kwneuro.cache) cache_dir (kwneuro.Cache attribute) (kwneuro.cache.Cache attribute) cacheable() (in module kwneuro) (in module kwneuro.cache) CacheSpec (class in kwneuro) (class in kwneuro.cache) CombatEstimates (class in kwneuro.harmonize) combine_csd_peaks_to_vector_volume() (in module kwneuro.csd)

combine_response_functions() (in module kwneuro.csd) compute_csd_fods() (in module kwneuro.csd) compute_csd_peaks() (in module kwneuro.csd) compute_mean_b0() (kwneuro.Dwi method) (kwneuro.dwi.Dwi method) concatenate() (kwneuro.Dwi static method) (kwneuro.dwi.Dwi static method) correct_bias() (kwneuro.structural.StructuralImage method) (kwneuro.StructuralImage method) create_estimate_volume_resource() (in module kwneuro.util)

D

deep_equal_allclose() (in module kwneuro.util) denoise() (kwneuro.Dwi method) (kwneuro.dwi.Dwi method) denoise_dwi() (in module kwneuro.denoise)

directions (kwneuro.noddi.Noddi attribute) Dti (class in kwneuro.dti) Dwi (class in kwneuro) (class in kwneuro.dwi)

E

ensure_output_dir() (in module kwneuro.util) estimate_dti() (kwneuro.dti.Dti static method) (kwneuro.Dwi method) (kwneuro.dwi.Dwi method) estimate_noddi() (kwneuro.Dwi method) (kwneuro.dwi.Dwi method) (kwneuro.noddi.Noddi static method)

estimate_response_function() (in module kwneuro.csd) estimates (kwneuro.harmonize.CombatEstimates attribute) extract_brain() (kwneuro.Dwi method) (kwneuro.dwi.Dwi method) (kwneuro.structural.StructuralImage method) (kwneuro.StructuralImage method) extract_tractseg() (in module kwneuro.tractseg)

F

files (kwneuro.cache.CacheSpec attribute) (kwneuro.CacheSpec attribute) force (kwneuro.Cache attribute) (kwneuro.cache.Cache attribute) from_ants_image() (kwneuro.resource.InMemoryVolumeResource static method)

from_dipy_object() (kwneuro.resource.InMemoryResponseFunctionResource static method) from_prolate_tensor() (kwneuro.resource.InMemoryResponseFunctionResource static method) FslBvalResource (class in kwneuro.io) FslBvecResource (class in kwneuro.io) fwf (kwneuro.noddi.Noddi property)

G

get() (kwneuro.io.FslBvalResource method) (kwneuro.io.FslBvecResource method) (kwneuro.io.JsonResponseFunctionResource method) (kwneuro.resource.BvalResource method) (kwneuro.resource.BvecResource method) (kwneuro.resource.InMemoryBvalResource method) (kwneuro.resource.InMemoryBvecResource method) (kwneuro.resource.InMemoryResponseFunctionResource method) (kwneuro.resource.ResponseFunctionResource method) get_affine() (kwneuro.io.NiftiVolumeResource method) (kwneuro.resource.InMemoryVolumeResource method) (kwneuro.resource.VolumeResource method) get_array() (kwneuro.io.NiftiVolumeResource method) (kwneuro.resource.InMemoryVolumeResource method) (kwneuro.resource.VolumeResource method)

get_dipy_object() (kwneuro.io.JsonResponseFunctionResource method) (kwneuro.resource.InMemoryResponseFunctionResource method) (kwneuro.resource.ResponseFunctionResource method) get_eig() (kwneuro.dti.Dti method) get_fa_md() (kwneuro.dti.Dti method) get_gtab() (kwneuro.Dwi method) (kwneuro.dwi.Dwi method) get_metadata() (kwneuro.io.NiftiVolumeResource method) (kwneuro.resource.InMemoryVolumeResource method) (kwneuro.resource.VolumeResource method) get_modulated_ndi_odi() (kwneuro.noddi.Noddi method)

H

harmonize_volumes() (in module kwneuro.harmonize)

I

info (kwneuro.harmonize.CombatEstimates attribute) initialize_from_ants() (kwneuro.reg.TransformResource static method) InMemoryBvalResource (class in kwneuro.resource) InMemoryBvecResource (class in kwneuro.resource) InMemoryResponseFunctionResource (class in kwneuro.resource) InMemoryVolumeResource (class in kwneuro.resource) is_cached() (kwneuro.Cache method) (kwneuro.cache.Cache method) is_forced() (kwneuro.Cache method) (kwneuro.cache.Cache method)

is_loaded (kwneuro.io.FslBvalResource attribute) (kwneuro.io.FslBvecResource attribute) (kwneuro.io.JsonResponseFunctionResource attribute) (kwneuro.io.NiftiVolumeResource attribute) (kwneuro.resource.InMemoryBvalResource attribute) (kwneuro.resource.InMemoryBvecResource attribute) (kwneuro.resource.InMemoryResponseFunctionResource attribute) (kwneuro.resource.InMemoryVolumeResource attribute) (kwneuro.resource.Resource attribute)

J

JsonResponseFunctionResource (class in kwneuro.io)

K

kwneuro module kwneuro() (in module kwneuro.cli) kwneuro-dwi-denoise command line option --bval --bvec --dwi --out-dwi kwneuro-dwi-dti command line option --bval --bvec --dwi --mask --out-dti --out-fa --out-md kwneuro-dwi-mean-b0 command line option --bval --bvec --dwi --out kwneuro-mask-dwi-batch command line option --inputs --outputs --sequential kwneuro-mask-structural-batch command line option --inputs --outputs --sequential kwneuro-registration-apply command line option --fixed --interpolation --invert --moving --out --transform kwneuro-registration-dwi-to-structural command line option --bval --bvec --dwi --dwi-mask --out-transform --structural --structural-mask --transform kwneuro-registration-volumes command line option --fixed --mask --moving --moving-mask --out --out-transform --transform

kwneuro-structural-bias-correct command line option --image --out kwneuro-structural-extract-brain command line option --image --out-mask kwneuro-structural-parcellate command line option --image --method --out kwneuro-structural-segment-tissues command line option --image --mask --method --out kwneuro.build_template module kwneuro.cache module kwneuro.cli module kwneuro.csd module kwneuro.denoise module kwneuro.dti module kwneuro.dwi module kwneuro.external module kwneuro.files module kwneuro.harmonize module kwneuro.io module kwneuro.masks module kwneuro.noddi module kwneuro.reg module kwneuro.resource module kwneuro.structural module kwneuro.tractseg module kwneuro.util module

L

load (kwneuro.cache.CacheSpec attribute) (kwneuro.CacheSpec attribute) load() (kwneuro.dti.Dti method) (kwneuro.Dwi method) (kwneuro.dwi.Dwi method) (kwneuro.io.FslBvalResource method) (kwneuro.io.FslBvecResource method) (kwneuro.io.JsonResponseFunctionResource method) (kwneuro.io.NiftiVolumeResource method) (kwneuro.noddi.Noddi method) (kwneuro.reg.TransformResource class method) (kwneuro.resource.BvalResource method) (kwneuro.resource.BvecResource method) (kwneuro.resource.InMemoryVolumeResource method) (kwneuro.resource.Resource method) (kwneuro.resource.ResponseFunctionResource method) (kwneuro.resource.VolumeResource method) (kwneuro.structural.StructuralImage method) (kwneuro.StructuralImage method)

M

matrices (kwneuro.reg.TransformResource property) metadata (kwneuro.resource.InMemoryVolumeResource attribute) module kwneuro kwneuro.build_template kwneuro.cache kwneuro.cli kwneuro.csd kwneuro.denoise kwneuro.dti kwneuro.dwi kwneuro.external kwneuro.files kwneuro.harmonize kwneuro.io kwneuro.masks kwneuro.noddi kwneuro.reg kwneuro.resource kwneuro.structural kwneuro.tractseg kwneuro.util

N

ndi (kwneuro.noddi.Noddi property) NiftiVolumeResource (class in kwneuro.io)

Noddi (class in kwneuro.noddi) normalize_path() (in module kwneuro.util)

O

odi (kwneuro.noddi.Noddi property)

P

parcellate() (kwneuro.structural.StructuralImage method) (kwneuro.StructuralImage method) path (kwneuro.io.FslBvalResource attribute) (kwneuro.io.FslBvecResource attribute) (kwneuro.io.JsonResponseFunctionResource attribute) (kwneuro.io.NiftiVolumeResource attribute)

path_in (kwneuro.io.FslBvalResource attribute) (kwneuro.io.FslBvecResource attribute) (kwneuro.io.JsonResponseFunctionResource attribute) (kwneuro.io.NiftiVolumeResource attribute) PathLike (in module kwneuro.util)

R

read_dwi_fsl() (in module kwneuro) (in module kwneuro.files) read_structural() (in module kwneuro) (in module kwneuro.files) read_volume() (in module kwneuro) (in module kwneuro.files)

register_dwi_to_structural() (in module kwneuro.reg) register_volumes() (in module kwneuro.reg) register_volumes_multimetric() (in module kwneuro.reg) Resource (class in kwneuro.resource) ResponseFunctionResource (class in kwneuro.resource)

S

save (kwneuro.cache.CacheSpec attribute) (kwneuro.CacheSpec attribute) save() (kwneuro.dti.Dti method) (kwneuro.Dwi method) (kwneuro.dwi.Dwi method) (kwneuro.io.FslBvalResource static method) (kwneuro.io.FslBvecResource static method) (kwneuro.io.JsonResponseFunctionResource static method) (kwneuro.io.NiftiVolumeResource static method) (kwneuro.noddi.Noddi method) (kwneuro.reg.TransformResource method) (kwneuro.structural.StructuralImage method) (kwneuro.StructuralImage method)

segment_tissues() (kwneuro.structural.StructuralImage method) (kwneuro.StructuralImage method) sh_coeffs (kwneuro.resource.InMemoryResponseFunctionResource attribute) status() (kwneuro.Cache method) (kwneuro.cache.Cache method) step_name (kwneuro.cache.CacheSpec attribute) (kwneuro.CacheSpec attribute) StructuralImage (class in kwneuro) (class in kwneuro.structural) subsample_dwi() (in module kwneuro.dwi) subsample_volume() (in module kwneuro.util)

T

T (in module kwneuro.cache) temporary_dwi_files() (in module kwneuro.external) temporary_structural_file() (in module kwneuro.external) temporary_volume_file() (in module kwneuro.external)

TemporaryDwiFiles (class in kwneuro.external) to_ants_image() (kwneuro.resource.InMemoryVolumeResource method) TRANSFORM_MANIFEST (in module kwneuro.reg) TransformResource (class in kwneuro.reg)

U

update_volume_metadata() (in module kwneuro.util)

V

volume (kwneuro.dti.Dti attribute) (kwneuro.Dwi attribute) (kwneuro.dwi.Dwi attribute) (kwneuro.external.TemporaryDwiFiles attribute) (kwneuro.noddi.Noddi attribute) (kwneuro.structural.StructuralImage attribute) (kwneuro.StructuralImage attribute)

VolumeResource (class in kwneuro.resource)

W

warp_fields (kwneuro.reg.TransformResource property) write_dwi_fsl() (in module kwneuro) (in module kwneuro.files)

write_structural() (in module kwneuro) (in module kwneuro.files) write_volume() (in module kwneuro) (in module kwneuro.files)