Index

A

AnatomicalPipeline (class in pymialsrtk.pipelines.anatomical.srr)

B

bids_dir (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute) binarize_image() (in module pymialsrtk.interfaces.postprocess)

BrainExtraction BtkNLMDenoising

C

create_docker_cmd() (in module pymialsrtk.cli.mialsuperresolutiontoolkit_docker)

create_singularity_cmd() (in module pymialsrtk.cli.mialsuperresolutiontoolkit_singularity) create_workflow() (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline method)

D

deltatTV (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)

F

FilenamesGeneration

FilteringByRunid

L

lambdaTV (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)

M

m_do_refine_hr_mask (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute) m_masks_derivatives_dir (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute) m_out_files (pymialsrtk.interfaces.reconstruction.MialsrtkTVSuperResolution attribute) m_output_dict (pymialsrtk.interfaces.reconstruction.MialsrtkTVSuperResolution attribute) m_output_files (pymialsrtk.interfaces.preprocess.FilteringByRunid attribute) m_skip_nlm_denoising (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute) m_skip_stacks_ordering (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute) m_skip_svr (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute) m_stack_order (pymialsrtk.interfaces.preprocess.StacksOrdering attribute) m_stacks (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute) m_substitutions (pymialsrtk.interfaces.postprocess.FilenamesGeneration attribute) main() (in module pymialsrtk.cli.mialsuperresolutiontoolkit_docker) (in module pymialsrtk.cli.mialsuperresolutiontoolkit_singularity) MialsrtkCorrectSliceIntensity

MialsrtkHistogramNormalization MialsrtkImageReconstruction MialsrtkIntensityStandardization MialsrtkMaskImage MialsrtkN4BiasFieldCorrection MialsrtkRefineHRMaskByIntersection MialsrtkSliceBySliceCorrectBiasField MialsrtkSliceBySliceN4BiasFieldCorrection MialsrtkTVSuperResolution MultipleBrainExtraction MultipleBtkNLMDenoising MultipleMialsrtkCorrectSliceIntensity MultipleMialsrtkMaskImage MultipleMialsrtkSliceBySliceCorrectBiasField MultipleMialsrtkSliceBySliceN4BiasFieldCorrection

O

output_dir (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)

P

primal_dual_loops (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute) pymialsrtk.cli.mialsuperresolutiontoolkit_docker (module) pymialsrtk.cli.mialsuperresolutiontoolkit_singularity (module) pymialsrtk.interfaces.postprocess (module)

pymialsrtk.interfaces.preprocess (module) pymialsrtk.interfaces.reconstruction (module) pymialsrtk.interfaces.utils (module) pymialsrtk.pipelines.anatomical.srr (module)

R

reorder_by_run_ids() (in module pymialsrtk.interfaces.utils)

run() (in module pymialsrtk.interfaces.utils) (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline method)

S

session (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute) sort_ascending() (in module pymialsrtk.interfaces.utils)

sr_id (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute) StacksOrdering subject (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)

U

use_manual_masks (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)

W

wf (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)