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README.md

What is SAGIT

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.

Setup

Requirements

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

Install

environment

First make sure python>2.6

In .bashrc, create entries for SLICER_4HOME:

export SLICER4_HOME="/path/to/slice4"

SAGIT setup

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