Getting started
Installation Instructions for Users
User Documentation
BIDS and BIDS App standards
Commandline Usage
Outputs of MIALSRTK BIDS App
API Documentation
Command-line interface (CLI) module
Preprocess module
Postprocess module
Reconstruction module
Utility (utils) module
Pipelines module
About MIALSRTK
BSD 3-Clause License
Citing
Changes
Contributing
Contributors
Medical Image Analysis Laboratory Super-Resolution Toolkit
»
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
F
|
G
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
U
|
W
A
AnatomicalPipeline (class in pymialsrtk.pipelines.anatomical.srr)
,
[1]
B
bids_dir (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
BinarizeImage
,
[1]
BrainExtraction
,
[1]
BtkNLMDenoising
,
[1]
C
create_docker_cmd() (in module pymialsrtk.cli.mialsuperresolutiontoolkit_docker)
,
[1]
create_singularity_cmd() (in module pymialsrtk.cli.mialsuperresolutiontoolkit_singularity)
,
[1]
create_subject_report() (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline method)
,
[1]
create_workflow() (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline method)
,
[1]
D
deltatTV (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
F
FilenamesGeneration
,
[1]
FilteringByRunid
,
[1]
G
get_parser() (in module pymialsrtk.parser)
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_masks_desc (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
m_out_files (pymialsrtk.interfaces.reconstruction.MialsrtkTVSuperResolution attribute)
,
[1]
m_output_dict (pymialsrtk.interfaces.reconstruction.MialsrtkTVSuperResolution attribute)
,
[1]
m_output_files (pymialsrtk.interfaces.preprocess.FilteringByRunid attribute)
,
[1]
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)
,
[1]
m_stacks (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
m_substitutions (pymialsrtk.interfaces.postprocess.FilenamesGeneration attribute)
,
[1]
main() (in module pymialsrtk.cli.mialsuperresolutiontoolkit_docker)
,
[1]
(in module pymialsrtk.cli.mialsuperresolutiontoolkit_singularity)
,
[1]
MialsrtkCorrectSliceIntensity
,
[1]
MialsrtkHistogramNormalization
,
[1]
MialsrtkImageReconstruction
,
[1]
MialsrtkIntensityStandardization
,
[1]
MialsrtkMaskImage
,
[1]
MialsrtkN4BiasFieldCorrection
,
[1]
MialsrtkRefineHRMaskByIntersection
,
[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.srr
,
[1]
MultipleBrainExtraction
,
[1]
MultipleBtkNLMDenoising
,
[1]
MultipleMialsrtkCorrectSliceIntensity
,
[1]
MultipleMialsrtkMaskImage
,
[1]
MultipleMialsrtkSliceBySliceCorrectBiasField
,
[1]
MultipleMialsrtkSliceBySliceN4BiasFieldCorrection
,
[1]
N
nipype_number_of_cores (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
O
openmp_number_of_cores (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
output_dir (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
P
pipeline_name (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
primal_dual_loops (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline 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.srr
module
,
[1]
R
reorder_by_run_ids() (in module pymialsrtk.interfaces.utils)
,
[1]
run() (in module pymialsrtk.interfaces.utils)
,
[1]
(pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline method)
,
[1]
run_elapsed_time (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
run_end_time (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
run_start_time (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
S
session (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
sort_ascending() (in module pymialsrtk.interfaces.utils)
,
[1]
sr_id (pymialsrtk.pipelines.anatomical.srr.AnatomicalPipeline attribute)
StacksOrdering
,
[1]
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)
write_bids_derivative_description() (in module pymialsrtk.bids.utils)
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v: v2.0.2
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