The Stanford MRS Analysis Library (SMAL)
Analysis of data from MR spectroscopy experiments.
For usage, please refer to the online documentation.
Using SMAL requires the following scientific python software packages: numpy, scipy, matplotlib. The easiest way to install these for most platforms is using the free Anaconda or Canopy software distributions.
In addition, the software requires the nibabel and nitime neuroimaging
libraries. These are most easily installed using
pip. As in:
pip install nibabel pip install nipype
Additional, optional, requirements (used in some functions) are nipype, together with FSL and Freesurfer, as well as IPython (which is used to run the examples).
To install from source make sure that you have all the dependencies installed, then clone this repository and run:
python setup.py install
mrs-analysis: This is a little command-line utility that takes nifti files as
input and produces a
csv file as output, with the ppm scale and the spectra
from the two measurement echos. See
mrs-analyze --help for help.
LICENSE for details.
(C) Ariel Rokem, Grace Tang, Center for Cognitive and Neurobiological Imaging, Stanford University 2013