Index

A

AbstractAnatomicalPipeline (class in pymialsrtk.pipelines.anatomical.abstract), [1]

add_directive_header() (pymialsrtk.sphinxext.documenter.NipypeClassDocumenter method) ApplyAlignmentTransform, [1]

B

BinarizeImage, [1]

BrainExtraction, [1] BtkNLMDenoising, [1]

C

check_parameters_integrity() (pymialsrtk.pipelines.anatomical.preprocessing.PreprocessingPipeline method), [1] CheckAndFilterInputStacks, [1] ComputeAlignmentToReference, [1] ConcatenateImageMetrics, [1] convert_ga() (in module pymialsrtk.workflows.postproc_stage) create_docker_cmd() (in module pymialsrtk.cli.mialsuperresolutiontoolkit_docker), [1] create_input_stage() (in module pymialsrtk.workflows.input_stage), [1] create_postproc_stage() (in module pymialsrtk.workflows.postproc_stage) create_preproc_output_stage() (in module pymialsrtk.workflows.output_stage), [1]

create_preproc_stage() (in module pymialsrtk.workflows.preproc_stage), [1] create_recon_labelmap_stage() (in module pymialsrtk.workflows.recon_labelmap_stage), [1] create_recon_stage() (in module pymialsrtk.workflows.recon_stage), [1] create_registration_stage() (in module pymialsrtk.workflows.registration_stage), [1] create_singularity_cmd() (in module pymialsrtk.cli.mialsuperresolutiontoolkit_singularity), [1] create_srr_assessment_stage() (in module pymialsrtk.workflows.srr_assessment_stage), [1] create_srr_output_stage() (in module pymialsrtk.workflows.output_stage), [1] create_workflow() (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline method), [1] (pymialsrtk.pipelines.anatomical.preprocessing.PreprocessingPipeline method), [1] (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline method), [1]

F

FilenamesGeneration, [1]

G

get_emission_car_miles_equivalent() (in module pymialsrtk.interfaces.utils), [1] get_emission_tv_time_equivalent() (in module pymialsrtk.interfaces.utils), [1] get_empty_ref_image() (pymialsrtk.interfaces.reconstruction.MialsrtkSDIComputation method), [1]

get_parser() (in module pymialsrtk.parser) get_singularity_wrapper_parser() (in module pymialsrtk.parser) get_url() (in module pymialsrtk.sphinxext.gh) get_wrapper_parser() (in module pymialsrtk.parser)

I

ImageMetrics, [1]

L

ListsMerger, [1]

M

m_best_transform (pymialsrtk.interfaces.preprocess.ComputeAlignmentToReference attribute), [1] m_bids_dir (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_do_anat_orientation (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_do_multi_parameters (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_do_nlm_denoising (pymialsrtk.pipelines.anatomical.preprocessing.PreprocessingPipeline attribute) (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_do_refine_hr_mask (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_do_registration (pymialsrtk.pipelines.anatomical.preprocessing.PreprocessingPipeline attribute) m_do_srr_assessment (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_final_res_dir (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_keep_all_outputs (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_labels_derivatives_dir (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_list_of_files (pymialsrtk.interfaces.preprocess.ListsMerger attribute), [1] m_masks_derivatives_dir (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_masks_desc (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_nipype_number_of_cores (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_openmp_number_of_cores (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_out_files (pymialsrtk.interfaces.reconstruction.MialsrtkTVSuperResolution attribute), [1] m_output_dict (pymialsrtk.interfaces.reconstruction.MialsrtkTVSuperResolution attribute), [1] m_output_dir (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_output_images (pymialsrtk.interfaces.preprocess.CheckAndFilterInputStacks attribute), [1] m_output_labels (pymialsrtk.interfaces.preprocess.CheckAndFilterInputStacks attribute), [1] m_output_masks (pymialsrtk.interfaces.preprocess.CheckAndFilterInputStacks attribute), [1] m_output_stacks (pymialsrtk.interfaces.preprocess.CheckAndFilterInputStacks attribute), [1] m_paramTV (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_pipeline_name (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) (pymialsrtk.pipelines.anatomical.preprocessing.PreprocessingPipeline attribute) (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_run_elapsed_time (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_run_end_time (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_run_start_time (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_session (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_skip_stacks_ordering (pymialsrtk.pipelines.anatomical.preprocessing.PreprocessingPipeline attribute) (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_skip_svr (pymialsrtk.pipelines.anatomical.preprocessing.PreprocessingPipeline attribute) (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline attribute) m_sr_id (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_stack_order (pymialsrtk.interfaces.preprocess.StacksOrdering attribute), [1] m_stacks (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_sub_path (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_sub_ses (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_subject (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_substitutions (pymialsrtk.interfaces.postprocess.FilenamesGeneration attribute), [1] m_TV_parameters (pymialsrtk.interfaces.reconstruction.MialsrtkTVSuperResolution attribute), [1] m_use_manual_masks (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_verbose (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) m_wf (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute)

m_wf_base_dir (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline attribute) main() (in module pymialsrtk.cli.mialsuperresolutiontoolkit_docker), [1] (in module pymialsrtk.cli.mialsuperresolutiontoolkit_singularity), [1] MergeMajorityVote, [1] MialsrtkCorrectSliceIntensity, [1] MialsrtkHistogramNormalization, [1] MialsrtkImageReconstruction, [1] MialsrtkIntensityStandardization, [1] MialsrtkMaskImage, [1] MialsrtkN4BiasFieldCorrection, [1] MialsrtkRefineHRMaskByIntersection, [1] MialsrtkSDIComputation, [1] MialsrtkSliceBySliceCorrectBiasField, [1] MialsrtkSliceBySliceN4BiasFieldCorrection, [1] MialsrtkTVSuperResolution, [1] module pymialsrtk pymialsrtk.bids pymialsrtk.bids.utils pymialsrtk.cli pymialsrtk.cli.mialsuperresolutiontoolkit_docker, [1] pymialsrtk.cli.mialsuperresolutiontoolkit_singularity, [1] pymialsrtk.info pymialsrtk.interfaces pymialsrtk.interfaces.postprocess, [1] pymialsrtk.interfaces.preprocess, [1] pymialsrtk.interfaces.reconstruction, [1] pymialsrtk.interfaces.utils, [1] pymialsrtk.parser pymialsrtk.pipelines pymialsrtk.pipelines.anatomical pymialsrtk.pipelines.anatomical.abstract, [1] pymialsrtk.pipelines.anatomical.preprocessing, [1] pymialsrtk.pipelines.anatomical.srr, [1] pymialsrtk.sphinxext pymialsrtk.sphinxext.documenter pymialsrtk.sphinxext.gh pymialsrtk.utils pymialsrtk.workflows pymialsrtk.workflows.input_stage, [1] pymialsrtk.workflows.output_stage, [1] pymialsrtk.workflows.postproc_stage pymialsrtk.workflows.preproc_stage, [1] pymialsrtk.workflows.recon_labelmap_stage, [1] pymialsrtk.workflows.recon_stage, [1] pymialsrtk.workflows.registration_stage, [1] pymialsrtk.workflows.srr_assessment_stage, [1]

N

NipypeClassDocumenter (class in pymialsrtk.sphinxext.documenter)

norm_data() (pymialsrtk.interfaces.postprocess.ImageMetrics method), [1]

P

PreprocessingPipeline (class in pymialsrtk.pipelines.anatomical.preprocessing), [1] priority (pymialsrtk.sphinxext.documenter.NipypeClassDocumenter attribute) pymialsrtk module pymialsrtk.bids module pymialsrtk.bids.utils module pymialsrtk.cli module pymialsrtk.cli.mialsuperresolutiontoolkit_docker module, [1] pymialsrtk.cli.mialsuperresolutiontoolkit_singularity module, [1] pymialsrtk.info module pymialsrtk.interfaces module pymialsrtk.interfaces.postprocess module, [1] pymialsrtk.interfaces.preprocess module, [1] pymialsrtk.interfaces.reconstruction module, [1] pymialsrtk.interfaces.utils module, [1] pymialsrtk.parser module pymialsrtk.pipelines module pymialsrtk.pipelines.anatomical module

pymialsrtk.pipelines.anatomical.abstract module, [1] pymialsrtk.pipelines.anatomical.preprocessing module, [1] pymialsrtk.pipelines.anatomical.srr module, [1] pymialsrtk.sphinxext module pymialsrtk.sphinxext.documenter module pymialsrtk.sphinxext.gh module pymialsrtk.utils module pymialsrtk.workflows module pymialsrtk.workflows.input_stage module, [1] pymialsrtk.workflows.output_stage module, [1] pymialsrtk.workflows.postproc_stage module pymialsrtk.workflows.preproc_stage module, [1] pymialsrtk.workflows.recon_labelmap_stage module, [1] pymialsrtk.workflows.recon_stage module, [1] pymialsrtk.workflows.registration_stage module, [1] pymialsrtk.workflows.srr_assessment_stage module, [1]

R

ReduceFieldOfView, [1] reorder_by_run_ids() (in module pymialsrtk.interfaces.utils), [1] ReportGeneration, [1]

ResampleImage, [1] run() (in module pymialsrtk.interfaces.utils), [1] (pymialsrtk.pipelines.anatomical.abstract.AbstractAnatomicalPipeline method), [1] (pymialsrtk.pipelines.anatomical.srr.SRReconPipeline method), [1]

S

setup() (in module pymialsrtk.sphinxext.documenter) sort_ascending() (in module pymialsrtk.interfaces.utils), [1]

SplitLabelMaps, [1] SRReconPipeline (class in pymialsrtk.pipelines.anatomical.srr), [1] StacksOrdering, [1]

W

write_bids_derivative_description() (in module pymialsrtk.bids.utils)