dmrimatlab
This is a complete Matlab toolbox for basic-to-advanced diffusion MRI reconstruction, processing, and representation (see complete description in: http://www.lpi.tel.uva.es/dmrilab).
It includes:
- The classical Diffusion Tensor Imaging (DTI) formalism with linear and non-linear signal fitting.
- High Angular Resolution Diffusion Imaging (HARDI): - Spherical Harmonics (SH). - Orientation Probability Density Transform (OPDT). - Higher Order Tensors (HOT).
- (Constrained, regularized) Diffusion Spectrum Imaging (DSI).
- Spherical Means and Spherical Deconvolution (MiSFIT).
- (Constrained, regularized) Mean Apparent Propagator MRI (MAP-MRI/MAPL).
- Free-water elimination.
- Denoising of Diffusion Weighted Images.
- Representation of scalar maps, color-by-orientation, DTI glyphs, or ODF fields.
The toolbox is designed pursuing computational performance, so that large databases can be processed within a reasonable time to perform group studies, connectomics, atlasing or IA training afterwards. This is attained by coding the key parts of the algorithms as (efficiently) multi-threaded C/C++ mex code, and exploiting advanced BLAS/LAPACK optimizations when possible.
Authors:
Antonio Tristán Vega, Santiago Aja-Fernández, Guillem París.
Laboratorio de Procesado de Imagen. Universidad de Valladolid
Spain
In case you use the package for your own research, we ask you to kindly cite it as:
Antonio Tristán-Vega, Santiago Aja-Fernández and Guillem París. "dMRI-Lab: advanced diffusion MRI with Matlab" [Online resource] https://www.lpi.tel.uva.es/dmrilab January 2022. Universidad de Valladolid. Spain
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Download the code from https://github.com/atriveg/dmrimatlab.
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From the Matlab command window, cd to the home folder, i.e. that containing the setup script "setup__DMRIMatlab_toolbox.m".
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Run the setup script as either:
>> setup__DMRIMatlab_toolbox('useparallel',true); >> setup__DMRIMatlab_toolbox('useparallel',false);
or simply:
>> setup__DMRIMatlab_toolbox;
for using/avoid using the Parallel Computing Toolbox. In case you don't have a working license for it, the script will not throw an error. This will setup your Matlab path for the present session (it won't make any permanent changes).
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Download the test data used for demo files and tests by running [YOU ONLY NEED TO (SUCCESSFULLY) RUN THIS COMMAND ONCE]:
>> download_dmritestdata
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Make sure you have a suitable C/C++ compiler installed in your computer (in Windows, we recommend installing the "MinGW" Add-On from the Matlab interface).
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Run the script [YOU ONLY NEED TO RUN THIS COMMAND EACH TIME YOU PULL A NEW VERSION FROM THE REPO]:
>> makefile_mexcode
which will build all the necessary mex files within the toolbox.
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Open/run some of the demo files in the "examples" folder to get started.
引用格式
Antonio Tristán-Vega, Santiago Aja-Fernández and Guillem París. "dMRI-Lab: advanced diffusion MRI with Matlab" [Online resource] https://www.lpi.tel.uva.es/dmrilab March 2024. Universidad de Valladolid. Spain
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HYDI-DSI
HYDI-DSI/utils
MAPL
MiSFIT
MiSFIT/experimental
MiSFIT/utils
MiSFIT/utils/experimental
examples
freewater
gradients
graphics
hot
io
io/3rdparty/Nifti
io/3rdparty/Slicer-4.5/Extensions-24973/MatlabBridge/lib/Slicer-4.5/cli-modules/commandserver
io/3rdparty/Slicer-4.5/Extensions-24973/MatlabModules
logo
maths/laguerre
maths/legendre
maths/polyhedra
maths/sh
mexcode
noise
sh
tensor
tests
utils
examples
无法下载基于 GitHub 默认分支的版本
版本 | 已发布 | 发行说明 | |
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1.0.8 | Now the MAP-MRI/MAPL module is able to reconstruct the Ensemble Average Propagator (EAP) and the Orientation Distribution Function (ODF) |
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1.0.7 | Added MAP-MRI/MAPL module. Improved quadratic programming for HYDI-DSI |
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1.0.6 | Improved performance of multi-threaded mex files. Multi-threading is now available for all platforms (Linux, Win64, MAC) |
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1.0.5 | Demo for DT-MRI processing |
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1.0.4 | Added bibliographic notes |
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1.0.3 | Added auto-download of test data |
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1.0.2 | Changed readme |
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1.0.1 | Changed logo |
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1.0.0 |
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