shimming-toolbox
Overview
Welcome to shimming-toolbox!
Features
Installation
Usage
Getting Started
Installing shimming-toolbox
Mac
1. Set Up a Virtual Environment
Bash
Zsh
2. Install dcm2niix
3. Install FSL
4. Install from GitHub
5. Test the Install (optional)
Comprehensive Test
Testing subsets of soft dependencies
Linux
1. Set Up a Virtual Environment
2. Install dcm2niix
3. Install FSL
4. Install from GitHub
5. Test the Install (optional)
Comprehensive Test
Testing subsets of soft dependencies
Installing FSLeyes Plugin
Getting Started
demo_realtime_shimming.sh
Flowchart
Help
Developer Section
Contributing to shimming-toolbox
Introduction
Opening an issue
Before Submitting a New Issue
Submitting an Issue
Issue Examples
Opening a Branch
Developing
Pre-commit checks
Conflicts
Code style
Documentation and docstrings
Testing
Licensing
Committing
Commit Titles
Commit Sequences
Submitting a Pull Request
PR Labels
Work in progress
Continuous Integration
Reviewers
Merging your PR
Versioning
Contributors
CLI Reference
Fieldmapping
st_prepare_fieldmap
Shimming
st_realtime_shim
Masking
st_mask
box
rect
sct
threshold
File Conversion
st_dicom_to_nifti
Image manipulation
st_image
concat
st_maths
mean
Miscellaneous
st_download_data
System Tools
st_check_dependencies
st_dump_env_info
API Reference
Fieldmapping
Masking
Coils
Shim
Optimizer
Image manipulation
Numerical model
Miscellaneous
About
License and Warranty
shimming-toolbox
»
Index
Edit on GitHub
Index
Symbols
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_
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A
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B
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C
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D
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
Symbols
--anat <fname_anat>
st_realtime_shim command line option
--axis <axis>
st_image-concat command line option
st_maths-mean command line option
--brain <brain>
st_mask-sct command line option
--center <center>
st_mask-box command line option
st_mask-rect command line option
--centerline <centerline>
st_mask-sct command line option
--config <fname_config>
st_dicom_to_nifti command line option
--contrast <contrast>
st_mask-sct command line option
--dont-remove-tmp
st_dicom_to_nifti command line option
--file-centerline <file_centerline>
st_mask-sct command line option
--fmap <fname_fmap>
st_realtime_shim command line option
--gaussian-filter <gaussian_filter>
st_prepare_fieldmap command line option
--input <fname_input>
st_mask-box command line option
st_mask-rect command line option
st_mask-sct command line option
st_mask-threshold command line option
st_maths-mean command line option
--input <path_dicom>
st_dicom_to_nifti command line option
--kernel <kernel>
st_mask-sct command line option
--mag <fname_mag>
st_prepare_fieldmap command line option
--mask <fname_mask>
st_prepare_fieldmap command line option
--mask-riro <fname_mask_anat_riro>
st_realtime_shim command line option
--mask-static <fname_mask_anat_static>
st_realtime_shim command line option
--output <fname_output>
st_image-concat command line option
st_mask-sct command line option
st_maths-mean command line option
st_prepare_fieldmap command line option
st_realtime_shim command line option
--output <output>
st_download_data command line option
st_mask-box command line option
st_mask-rect command line option
st_mask-threshold command line option
--output <path_nifti>
st_dicom_to_nifti command line option
--pixdim <pixdim>
st_image-concat command line option
--remove-tmp
st_dicom_to_nifti command line option
--remove-tmp <remove_tmp>
st_mask-sct command line option
--resp <fname_resp>
st_realtime_shim command line option
--shape <shape>
st_mask-sct command line option
--sigma <sigma>
st_prepare_fieldmap command line option
--size <size>
st_mask-box command line option
st_mask-rect command line option
st_mask-sct command line option
--subject <subject>
st_dicom_to_nifti command line option
--thr <thr>
st_mask-threshold command line option
--threshold <threshold>
st_prepare_fieldmap command line option
--unwrapper <unwrapper>
st_prepare_fieldmap command line option
--verbose
st_download_data command line option
--verbose <verbose>
st_mask-sct command line option
-i
st_dicom_to_nifti command line option
st_mask-box command line option
st_mask-rect command line option
st_mask-sct command line option
st_mask-threshold command line option
st_maths-mean command line option
-o
st_dicom_to_nifti command line option
st_download_data command line option
st_image-concat command line option
st_mask-box command line option
st_mask-rect command line option
st_mask-sct command line option
st_mask-threshold command line option
st_maths-mean command line option
st_prepare_fieldmap command line option
st_realtime_shim command line option
_
__init__() (shimmingtoolbox.coils.coil.Coil method)
(shimmingtoolbox.optimizer.basic_optimizer.Optimizer method)
(shimmingtoolbox.optimizer.lsq_optimizer.LsqOptimizer method)
A
add_suffix() (in module shimmingtoolbox.utils)
affine (shimmingtoolbox.coils.coil.Coil attribute)
B
biot_savart() (in module shimmingtoolbox.coils.biot_savart)
C
coef_channel_minmax (shimmingtoolbox.coils.coil.Coil attribute)
coef_sum_max (shimmingtoolbox.coils.coil.Coil attribute)
Coil (class in shimmingtoolbox.coils.coil)
coils (shimmingtoolbox.optimizer.basic_optimizer.Optimizer attribute)
concat_data() (in module shimmingtoolbox.image)
create_output_dir() (in module shimmingtoolbox.utils)
D
DATA
st_download_data command line option
data (shimmingtoolbox.pmu.PmuResp attribute)
dicom_to_nifti() (in module shimmingtoolbox.dicom_to_nifti)
dim (shimmingtoolbox.coils.coil.Coil attribute)
download_data() (in module shimmingtoolbox.download)
F
field_strength (shimmingtoolbox.simulate.numerical_model.NumericalModel attribute)
fname (shimmingtoolbox.pmu.PmuResp attribute)
G
gamma (shimmingtoolbox.simulate.numerical_model.NumericalModel attribute)
generate_deltaB0() (shimmingtoolbox.simulate.numerical_model.NumericalModel method)
generate_meshgrid() (in module shimmingtoolbox.coils.coordinates)
get_acquisition_times() (in module shimmingtoolbox.load_nifti)
H
handedness (shimmingtoolbox.simulate.numerical_model.NumericalModel attribute)
I
INPUT
st_image-concat command line option
install_data() (in module shimmingtoolbox.download)
interp_resp_trace() (shimmingtoolbox.pmu.PmuResp method)
iso_times_to_ms() (in module shimmingtoolbox.utils)
L
load_constraints() (shimmingtoolbox.coils.coil.Coil method)
load_nifti() (in module shimmingtoolbox.load_nifti)
LsqOptimizer (class in shimmingtoolbox.optimizer.lsq_optimizer)
M
measurement (shimmingtoolbox.simulate.numerical_model.NumericalModel attribute)
merge_coils() (shimmingtoolbox.optimizer.basic_optimizer.Optimizer method)
(shimmingtoolbox.optimizer.lsq_optimizer.LsqOptimizer method)
merged_bounds (shimmingtoolbox.optimizer.basic_optimizer.Optimizer attribute)
merged_coils (shimmingtoolbox.optimizer.basic_optimizer.Optimizer attribute)
module
shimmingtoolbox.coils.biot_savart
shimmingtoolbox.coils.coil
shimmingtoolbox.coils.coordinates
shimmingtoolbox.coils.siemens_basis
shimmingtoolbox.coils.spherical_harmonics
shimmingtoolbox.dicom_to_nifti
shimmingtoolbox.download
shimmingtoolbox.image
shimmingtoolbox.load_nifti
shimmingtoolbox.masking.shapes
shimmingtoolbox.masking.threshold
shimmingtoolbox.optimizer.basic_optimizer
shimmingtoolbox.optimizer.lsq_optimizer
shimmingtoolbox.optimizer.sequential
shimmingtoolbox.pmu
shimmingtoolbox.simulate.numerical_model
shimmingtoolbox.unwrap.prelude
shimmingtoolbox.unwrap.unwrap_phase
shimmingtoolbox.utils
N
NumericalModel (class in shimmingtoolbox.simulate.numerical_model)
O
optimize() (shimmingtoolbox.optimizer.basic_optimizer.Optimizer method)
(shimmingtoolbox.optimizer.lsq_optimizer.LsqOptimizer method)
optimize_slicewise() (in module shimmingtoolbox.optimizer.sequential)
Optimizer (class in shimmingtoolbox.optimizer.basic_optimizer)
P
PHASE
st_prepare_fieldmap command line option
phys_gradient() (in module shimmingtoolbox.coils.coordinates)
phys_to_vox_gradient() (in module shimmingtoolbox.coils.coordinates)
PmuResp (class in shimmingtoolbox.pmu)
prelude() (in module shimmingtoolbox.unwrap.prelude)
profile (shimmingtoolbox.coils.coil.Coil attribute)
proton_density (shimmingtoolbox.simulate.numerical_model.NumericalModel attribute)
R
read_nii() (in module shimmingtoolbox.load_nifti)
read_resp() (shimmingtoolbox.pmu.PmuResp method)
required_constraints (shimmingtoolbox.coils.coil.Coil attribute)
resample_from_to() (in module shimmingtoolbox.coils.coordinates)
run_subprocess() (in module shimmingtoolbox.utils)
S
save() (shimmingtoolbox.simulate.numerical_model.NumericalModel method)
select_optimizer() (in module shimmingtoolbox.optimizer.sequential)
sequential_zslice() (in module shimmingtoolbox.optimizer.sequential)
shape_cube() (in module shimmingtoolbox.masking.shapes)
shape_square() (in module shimmingtoolbox.masking.shapes)
shapes() (in module shimmingtoolbox.masking.shapes)
shimmingtoolbox.coils.biot_savart
module
shimmingtoolbox.coils.coil
module
shimmingtoolbox.coils.coordinates
module
shimmingtoolbox.coils.siemens_basis
module
shimmingtoolbox.coils.spherical_harmonics
module
shimmingtoolbox.dicom_to_nifti
module
shimmingtoolbox.download
module
shimmingtoolbox.image
module
shimmingtoolbox.load_nifti
module
shimmingtoolbox.masking.shapes
module
shimmingtoolbox.masking.threshold
module
shimmingtoolbox.optimizer.basic_optimizer
module
shimmingtoolbox.optimizer.lsq_optimizer
module
shimmingtoolbox.optimizer.sequential
module
shimmingtoolbox.pmu
module
shimmingtoolbox.simulate.numerical_model
module
shimmingtoolbox.unwrap.prelude
module
shimmingtoolbox.unwrap.unwrap_phase
module
shimmingtoolbox.utils
module
siemens_basis() (in module shimmingtoolbox.coils.siemens_basis)
simulate_measurement() (shimmingtoolbox.simulate.numerical_model.NumericalModel method)
spherical_harmonics() (in module shimmingtoolbox.coils.spherical_harmonics)
st_dicom_to_nifti command line option
--config <fname_config>
--dont-remove-tmp
--input <path_dicom>
--output <path_nifti>
--remove-tmp
--subject <subject>
-i
-o
st_download_data command line option
--output <output>
--verbose
-o
DATA
st_image-concat command line option
--axis <axis>
--output <fname_output>
--pixdim <pixdim>
-o
INPUT
st_mask-box command line option
--center <center>
--input <fname_input>
--output <output>
--size <size>
-i
-o
st_mask-rect command line option
--center <center>
--input <fname_input>
--output <output>
--size <size>
-i
-o
st_mask-sct command line option
--brain <brain>
--centerline <centerline>
--contrast <contrast>
--file-centerline <file_centerline>
--input <fname_input>
--kernel <kernel>
--output <fname_output>
--remove-tmp <remove_tmp>
--shape <shape>
--size <size>
--verbose <verbose>
-i
-o
st_mask-threshold command line option
--input <fname_input>
--output <output>
--thr <thr>
-i
-o
st_maths-mean command line option
--axis <axis>
--input <fname_input>
--output <fname_output>
-i
-o
st_prepare_fieldmap command line option
--gaussian-filter <gaussian_filter>
--mag <fname_mag>
--mask <fname_mask>
--output <fname_output>
--sigma <sigma>
--threshold <threshold>
--unwrapper <unwrapper>
-o
PHASE
st_progress_bar() (in module shimmingtoolbox.utils)
st_realtime_shim command line option
--anat <fname_anat>
--fmap <fname_fmap>
--mask-riro <fname_mask_anat_riro>
--mask-static <fname_mask_anat_static>
--output <fname_output>
--resp <fname_resp>
-o
start_time_mdh (shimmingtoolbox.pmu.PmuResp attribute)
start_time_mpcu (shimmingtoolbox.pmu.PmuResp attribute)
stop_time_mdh (shimmingtoolbox.pmu.PmuResp attribute)
stop_time_mpcu (shimmingtoolbox.pmu.PmuResp attribute)
T
T2_star (shimmingtoolbox.simulate.numerical_model.NumericalModel attribute)
threshold() (in module shimmingtoolbox.masking.threshold)
U
unshimmed (shimmingtoolbox.optimizer.basic_optimizer.Optimizer attribute)
unshimmed_affine (shimmingtoolbox.optimizer.basic_optimizer.Optimizer attribute)
unwrap_phase() (in module shimmingtoolbox.unwrap.unwrap_phase)
unzip() (in module shimmingtoolbox.download)
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