The Stanford MRS Analysis Library (SMAL)

Analysis of data from MR spectroscopy experiments.

For usage, please refer to the online documentation.

Installation

Released versions

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).

From source

To install from source make sure that you have all the dependencies installed, then clone this repository and run:

python setup.py install

Usage

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