Download and Install¶
Download Links¶
Example Data and Test Script¶
- List File: list.txt [12 Bytes]
- Subject 01: sub01.tar.gz [87.1 MB]
- Subject 02: sub02.tar.gz [85.5 MB]
- Brain Atlas: atlas.tar.gz [1.57 MB]
- Test Script [ process_advanced.sh ] [ process_primary.sh ]
- List File: list.txt [12 Bytes]
- Subject 01: sub01.tar.gz [87.1 MB]
- Subject 02: sub02.tar.gz [85.5 MB]
- Brain Atlas: atlas.tar.gz [1.57 MB]
- Test Script [ process_advanced.sh ] [ process_primary.sh ]
And this is what we have in the data above:
├── atlas
│ ├── aal.nii.gz
│ ├── aal.nii.lut
│ ├── aal.nii.txt
│ ├── aal_roi_024.txt
│ ├── aal_roi_090.txt
│ ├── BN_Atlas_246_1mm.nii.gz
│ ├── BN_Atlas_246.txt
│ └── ch2bet.nii.gz
├── atlas.tar.gz
├── list.txt
├── process_advanced.sh
├── process_primary.sh
├── sub01
│ ├── dwi.bval
│ ├── dwi.bvec
│ ├── dwi.nii.gz
│ └── t1.nii.gz
├── sub01.tar.gz
├── sub02
│ ├── dwi.bval
│ ├── dwi.bvec
│ ├── dwi.nii.gz
│ └── t1.nii.gz
└── sub02.tar.gz
We recommand users to follow the Tutorial Page for a step-by-step introduction of the functions within DiffutionKit.
IN A HURRY? Download all the data files (REQUIRED) above and run the Bash script process_advanced.sh or process_primary.sh. These two scripts have exactly the same functions, except that the primary one is for those who don’t have too much background in Bash scripting and the advanced one is Makefile-based which avoids repeatly compiling the unchaged data in multiple compiles. Or simply run the following commands to do everything (for Linux ONLY).
# install DiffusionKit
kitv='v1.4-r161127' ## This line should be changed according to the version you desired.
kitname='DiffusionKitSetup-x86_64-'${kitv}
wget https://github.com/brainnetome/diffusionkit/releases/download/${kitv}/${kitname}'.tar.gz'
tar zxvf ${kitname}'.tar.gz'
export PATH=$PATH:$(pwd)/${kitname}/bin
# get the data and run!
wget https://github.com/brainnetome/diffusionkit/releases/download/v1.4-r161127/list.txt
wget https://github.com/brainnetome/diffusionkit/releases/download/v1.4-r161127/sub01.tar.gz
wget https://github.com/brainnetome/diffusionkit/releases/download/v1.4-r161127/sub02.tar.gz
wget https://github.com/brainnetome/diffusionkit/releases/download/v1.4-r161127/atlas.tar.gz
wget https://raw.githubusercontent.com/brainnetome/diffusionkit/master/source/static/process_advanced.sh
chmod +x process_advanced.sh
./process_advanced.sh
# install DiffusionKit
kitv='v1.3-r160923' ## CAUTION: This line should be changed according to the version.
kitname='DiffusionKitSetup-x86_64-'${kitv}
wget http://ddl.escience.cn/ff/emKy?func=download -O ${kitname}'.tar.gz'
tar zxvf ${kitname}'.tar.gz'
export PATH=$PATH:$(pwd)/${kitname}/bin
# get the data and run!
wget https://github.com/brainnetome/diffusionkit/releases/download/v1.3-r160923/list.txt
wget http://ddl.escience.cn/ff/emBl?func=download -O sub01.tar.gz
wget http://ddl.escience.cn/ff/emBm?func=download -O sub02.tar.gz
wget http://ddl.escience.cn/ff/emBo?func=download -O atlas.tar.gz
wget https://raw.githubusercontent.com/brainnetome/diffusionkit/master/source/static/process_advanced.sh
chmod +x process_advanced.sh
./process_advanced.sh
And more simpler way is to copy the code in the above panel (choose the server close to you) and save it as a file, such as test-diffusionkit.sh, or test-diffusionkit-china.sh. and run to take a quick look how DiffusionKit can BUILD A BRAIN NETWORK JUST A FEW MINUTES!
System requirement¶
Basically this software can run in any system, including 64-bit MS Windows/Linux OS, although currently we only tested and released the binary packages for Windows/Linux OS. The software is developed based on C/C++, and some platform independent packages, including VTK, and OpenCV, etc. However, for high-performance data processing and visualization, we recommend using 64-bit OS with multi-core CPU and standalone graphics card.
Install/Uninstall¶
Please download the package from http://diffusion.brainnetome.org , according to your own OS. Unpack the files to where you want and you can enjoy the software. The 64-bit OS is recommended for high-performance data processing. Each installation package is completely standalone so you DO NOT need to install ANY other dependency to run the software. If you encounter any dependency problem please DO contact us.
For MS Windows OS¶
Double click the DiffusionKitSetup-WIN64-v1.4-r161127.exe file and then choose the destination path
according to the wizard. You may need to provide administrator permission
if you want to put the files into the system path.
Similarly, to uninstall you only need to hit the menu of “uninstall” in the MS Windows start menu.
For Linux OS¶
Glibc>=2.2 is required. Download the DiffusionKitSetup-x86_64-v1.4-r161127.tar.gz, and then
tar zxvf DiffusionKitSetup-x86_64-v1.4-r161127.tar.gz
export PATH=$PATH:`pwd`/DiffusionKitSetup-x86_64-v1.4-r161127/bin
You could add the path to the $PATH in the ~/.bashrc file, by adding the following line,
export $PATH=$PATH:/your/path/to/diffusionkit
To uninstall the software, just manually remove the entire folder where you untar-ed the .tar.gz file.
The citation for DiffusionKit could be:
Sangma Xie, Liangfu Chen, Nianming Zuo and Tianzi Jiang, DiffusionKit: A Light One-Stop Solution for Diffusion MRI Data Analysis, Journal of Neuroscience Methods, vol. 273, pp. 107-119, 2016. [PDF] .