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

Setup the environment

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

Dependencies

1. Install the requirements with

   pip install -r requirements.txt
   

2. Two other required packages are pynrrd and fascicles, they can be found at:

   • https://github.com/sinkpoint/pynrrd
   • https://github.com/sinkpoint/fascicle

   Install them as well.

3. Then install the library

   python setup.py install