release-1.3.0
Getting started
Installing Nighres
Nighres usage examples
Modules and Functions
Brain
Cortex
Data
Filtering
Intensity
Input/Output
Laminar
Microscopy
Registration
Segmentation
Shape
Statistics
Surface
Good to know
Data handling and formats
Saving outputs
Levelsets
Developer's guide
Overview
Setting up
Wrapping an existing CBS Tools class
Adding a new Python function
Writing examples
Adapting the docs
Making a Pull Request
Nighres
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Index
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Index
A
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B
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C
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D
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E
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F
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G
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I
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L
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M
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P
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R
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S
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T
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V
A
apply_coordinate_mappings() (in module nighres.registration)
apply_coordinate_mappings_2d() (in module nighres.registration)
B
background_estimation() (in module nighres.intensity)
C
conditional_shape() (in module nighres.segmentation)
cruise_cortex_extraction() (in module nighres.cortex)
D
dots_segmentation() (in module nighres.brain)
download_7T_TRT() (in module nighres.data)
download_DOTS_atlas() (in module nighres.data)
download_DTI_2mm() (in module nighres.data)
E
embedded_antsreg() (in module nighres.registration)
embedded_antsreg_2d() (in module nighres.registration)
embedded_antsreg_multi() (in module nighres.registration)
extract_brain_region() (in module nighres.brain)
F
filter_ridge_structures() (in module nighres.filtering)
filter_stacking() (in module nighres.brain)
flash_t2s_fitting() (in module nighres.intensity)
fuzzy_cmeans() (in module nighres.segmentation)
G
generate_coordinate_mapping() (in module nighres.registration)
I
intensity_based_skullstripping() (in module nighres.brain)
intensity_propagation() (in module nighres.intensity)
L
laminar_iterative_smoothing() (in module nighres.laminar)
laminar_regional_approximation() (in module nighres.laminar)
lcat_denoising() (in module nighres.intensity)
lcpca_denoising() (in module nighres.intensity)
levelset_fusion() (in module nighres.shape)
levelset_to_mesh() (in module nighres.surface)
levelset_to_probability() (in module nighres.surface)
load_mesh_data() (in module nighres.io)
load_mesh_geometry() (in module nighres.io)
load_volume() (in module nighres.io)
M
mesh_to_levelset() (in module nighres.surface)
mgdm_cells() (in module nighres.microscopy)
mgdm_segmentation() (in module nighres.brain)
mp2rage_dura_estimation() (in module nighres.brain)
mp2rage_skullstripping() (in module nighres.brain)
mp2rage_t1_mapping() (in module nighres.intensity)
mp2rageme_pd_mapping() (in module nighres.intensity)
multiscale_vessel_filter() (in module nighres.filtering)
P
phase_unwrapping() (in module nighres.intensity)
probability_to_levelset() (in module nighres.surface)
profile_averaging() (in module nighres.laminar)
profile_meshing() (in module nighres.laminar)
profile_sampling() (in module nighres.laminar)
R
recursive_ridge_diffusion() (in module nighres.filtering)
S
save_mesh_data() (in module nighres.io)
save_mesh_geometry() (in module nighres.io)
save_volume() (in module nighres.io)
segmentation_statistics() (in module nighres.statistics)
simple_align() (in module nighres.registration)
simple_skeleton() (in module nighres.shape)
stack_intensity_regularisation() (in module nighres.microscopy)
surface_inflation() (in module nighres.surface)
surface_mesh_mapping() (in module nighres.surface)
surface_som_mapping() (in module nighres.surface)
T
t2s_optimal_combination() (in module nighres.intensity)
topology_correction() (in module nighres.shape)
total_variation_filtering() (in module nighres.filtering)
V
volume_som_mapping() (in module nighres.surface)
volumetric_layering() (in module nighres.laminar)
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