Loading fsl_mrsi Results

The FSL-MRS package tool fsl_mrsi fits MRSI data and outputs a folder structure containing:

  • the spectral fits (fit, baseline, and residual),

  • the (internally or water) scaled concentrations of each fitted and combined metabolite,

  • the fitting uncertainties for each metabolite and combined metabolite,

  • SNR and linewidth (FWHM) QC metrics for each metabolite.

This plugin provides an easy to use interface to load and view each of these outputs.

Loading the data

After loading some MRSI data (see Loading the Plugin) load the results by selecting the Load FSL-MRS fit in the Tools menu.

_images/fsl_mrsi_menu.png

Use the dialogue that opens to select the results directory produced by fsl_mrsi (it should contain concs, fit, qc, and uncertainties sub-directories).

_images/fsl_mrsi_load.png

The results data will now be loaded.

Fit

After the data has loaded the FSL-MRS fit will be displayed, in red, on top of the spectrum in the MRS View panel.

_images/mrsi_fit.png

Additionally the baseline (green) and residual (grey) will be displayed. Each line should update as the cursor is moved over each voxel in the orthographic view.

Metabolite and QC maps

The Load FSL-MRS fit action will also create a FSL-MRS Results panel adjacent to the orthographic view panel.

_images/results_panel.png

This panel allows the user to quickly load metabolite maps. For example selecting NAA+NAAG in the Metabolite drop-down and conc-internal will load the metabolite map of NAA+NAAG concentrations referenced to total creatine.

_images/metab_map_1.png

Selecting a different map (Cr & FWHM) will remove the previous metabolite map and load the new one. If you want to retain the previous map, untick Replace? before selecting a new map. Overlays can also be managed through the Overlay list panel.

_images/metab_map_2.png