/SC_dMRI

Spinal cord diffusion MRI preprocessing tool

Primary LanguagePythonMIT LicenseMIT

SC_dMRI

Spinal cord diffusion MRI preprocessing tool

Dependency

python 2.7:

Only tested on 2.7. I recommend pip for the following module installation.

  • numpy
  • scipy
  • nibabel
  • matplotlib

python-tk:

  • Ubuntu/Debian: sudo apt-get install python-tk
  • Fedora: yum install tkinter

FSL 5.0.x

4dfp

  • for DTI map generation with outlier rejection

Installation

We don't have any fancy installation method yet.

  1. Download to any directory: git clone git@github.com:junqianxulab/SC_dMRI.git
  2. Give executable permission to the main file: chmod +x {download_directory}/SC_dMRI/csp_preprocessing/spine_reg_gui.py
  3. Make a symbolic link in a user directory (e.g. ln -s {download_directory}/SC_dMRI/csp_preprocessing/spine_reg_gui.py ${HOME}/bin) or a system directory (e.g. ln -s {download_directory}/SC_dMRI/csp_preprocessing/spine_reg_gui.py /local/bin).
  • Note that the directory containing the symbolic link should be in a PATH environment.
  1. Try spine_reg_gui.py

Documentation

under construction