SAGIT stands for Selective Automated Group Integrated Tractography. It's a Python library that automates the generation of tractography for Neuroimaging research.
It's developed by David Qixiang Chen as part of his PhD thesis with Dr. Mojgan Hodaie at the University of Toronto.
It supports popular tractography methods:
- Single tensor tractography (DTI)
- Extended Streamline Tractography (XST)
- Constrained Spherical Convolutional tractogrpahy (CST)
See (https://sinkpoint.gitbooks.io/sagit/content/) for full documentation.
SAGIT is developed and tested on Ubuntu 14.04 LTS.
SAGIT relies on a number of neuroimaging software packages for its functionality:
- 3D Slicer 4 (DTI)
- Hodaie TEEM (XST)
- MRTrix 3 (CST)
- Freesurfer
- Anatomical Normalization Tools (ANTs)
As well as these python libraries
- nibabel
- dipy
- scipy
- numpy
- pyparsing
- jsoncomment
A full list of packages can be found in requirement.txt
First make sure python>2.6
In .bashrc, create entries for SLICER_4HOME:
export SLICER4_HOME="/path/to/slice4"
It's recommended to have an isolated python environment for SAGIT This can be done with virtualenvwrapper
pip intall virtualenvwrapper
Then create a new environment for SAGIT
mkvirtualenv sagit
Then in the future, to return to the python environment, use
workon sagit
Install the requirements with
pip install -r requirements.txt
Then install the library
python setup.py install