fsleyes-plugin-mrs 0.1.9

FSLeyes extension for viewing MRS(I) data formatted as NIfTI-MRS.

fsleyes-plugin-mrs

An FSLeyes plugin for viewing the NIfTI-MRS format.

This plugin adds an additional MRS specific view panel to FSLeyes which displays spectra in the frequency domain. Higher dimensions of data stored in NIfTI-MRS format may be explored.

This plugin also loads and displays results from FSL-MRS's mrsi fitting routine fsl_mrsi. The plugin displays the spectral fit for each voxel and creates an interface for loading output metabolite maps easily.

Installation

Relies on FSLeyes (version >= 1.0.10). This package must be installed in the same environment as FSLeyes is run from.

Install using conda, pip, or by cloning this repository. For full installation instructions please see the documentation.

Conda

After activating the target environment run

conda install -c conda-forge fsleyes-plugin-mrs

PyPI

pip install fsleyes-plugin-mrs

Cloning from git

git clone https://git.fmrib.ox.ac.uk/wclarke/fsleyes-plugin-mrs
cd fsleyes-plugin-mrs
pip install .

Quick start guide

For full instructions please see the documentation.

NIfTI-MRS viewer

Start the dedicated MRSView by selecting MRSView in the View menu.

Once open the NIfTI-MRS dimension selector can be opened by clicking the icon.

Alternatively, a built-in MRS layout can be loaded from the View - Layouts menu, or the command line using:

fsleyes -smrs ...

for example with data

fsleyes -smrs t1.nii.gz svs.nii.gz

MRSI results viewer

A results folder generated by FSL-MRS's fsl_mrsi script can be loaded by using the Tools - Load FSL-MRS fit menu item.

The spectral fit, baseline, and residual is displayed in the MRSView. Metabolite maps and QC metrics can be loaded using the FSL-MRS Results panel added to the bottom of the orthographic view.

Acknowledgements and referencing

If you use this tool in your research please cite: TBC

Thanks to Paul McCarthy for his significant input into development of this plugin.