Running a HERMES dataset through Gannet 3.0

One of the new features of Gannet 3.0 is the ability to process and quantify edited MRS data acquired by HERMES (1–3). Here is a quick "getting started" tutorial on running a GABA-/GSH-edited HERMES dataset:

  1. Download Gannet 3.0, placing the master folder at the top of your MATLAB's search path.
  2. Open GannetPreInitialise.m.
  3. Set to 'GABAGlx' and MRS_struct.p.target2 to 'GSH' (these are the defaults).
  4. Set MRS_struct.p.ONOFForder to 'offfirst' if running a Philips HERMES dataset, or 'onfirst' if running a GE HERMES dataset.
  5. Set MRS_struct.p.water_removal to 1 (this is the default).
  6. Set MRS_struct.p.AlignTo to 'SpecRegHERMES'.
  7. Set MRS_struct.p.HERMES to 1.
  8. Save your changes.
  9. Change your working directory to where your HERMES dataset is saved.
  10. To run GannetLoad on:
    1. GE data, run: MRS = GannetLoad({'HERMES_1.7'});
    2. Philips data (with a water reference), run MRS = GannetLoad({'HERMES_1_act.sdat'},{'HERMES_1_ref.sdat'});
  11. Then run GannetFit: MRS = GannetFit(MRS);


1. Chan KL, Puts NAJ, Schär M, Barker PB, Edden RAE. HERMES: Hadamard encoding and reconstruction of MEGA-edited spectroscopy. Magn. Reson. Med. 2016;76:11–19. doi: 10.1002/mrm.26233.

2. Saleh MG, Oeltzschner G, Chan KL, Puts NAJ, Mikkelsen M, Schär M, Harris AD, Edden RAE. Simultaneous edited MRS of GABA and glutathione. NeuroImage 2016;142:576–582. doi: 10.1016/j.neuroimage.2016.07.056.

3. Chan KL, Saleh MG, Oeltzschner G, Barker PB, Edden RAE. Simultaneous measurement of Aspartate, NAA, and NAAG using HERMES spectral editing at 3 Tesla. NeuroImage 2017;155:587–593. doi: 10.1016/j.neuroimage.2017.04.043.