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 
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.
2 maintainers
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