Running a GSH-edited MEGA-PRESS dataset through Gannet 3.0

We have improved the data processing and quantification routines for GSH-edited MEGA-PRESS data in Gannet 3.0. Here is a quick "getting started" tutorial on running a GSH-edited MEGA-PRESS 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 MRS_struct.p.target to 'GSH' (MRS_struct.p.target2 can be ignored).
  4. Set MRS_struct.p.ONOFForder to 'offfirst' or 'onfirst' depending on the order of the ON/OFF editing pulses in your MEGA-PRESS acquisition (typically this should be 'offfirst' for Philips data and 'onfirst' for GE/Siemens data).
  5. Set MRS_struct.p.water_removal to 1 (this is the default) to remove residual water in the difference spectrum.
  6. Set MRS_struct.p.AlignTo to 'SpecRegHERMES'. (We recently published a novel frequency-and-phase correction algorithm for multiplexed edited MRS data [1]; this method also works well with GSH-edited data and is recommended.)
  7. Set MRS_struct.p.GSH_model to 'SixGauss' (recommended for long-TE MEGA-PRESS data).
  8. Save your changes.
  9. Change your working directory to where your GSH dataset is saved.
  10. To run GannetLoad on:
    1. GE data, run: MRS = GannetLoad({'GSH_MEGA_1.7'});
    2. Philips SDAT data (no water reference), run: MRS = GannetLoad({'GSH_MEGA_1_act.sdat'});
    3. Philips SDAT data (with water reference), run: MRS = GannetLoad({'GSH_MEGA_1_act.sdat'}, {'GSH_MEGA_1_ref.sdat'});
    4. Philips .data files (no water reference), run: MRS = GannetLoad({'GSH_MEGA_1.data'});
    5. Philips .data files (with water reference), run: MRS = GannetLoad({'GSH_MEGA_1.data'}, {'GSH_MEGA_1_water.data'});
    6. Siemens .rda data (no water reference), run: MRS = GannetLoad({'GSH_MEGA_1_ON.rda', 'GSH_MEGA_1_OFF.rda'});
    7. Siemens .rda data (with water reference), run: MRS = GannetLoad({'GSH_MEGA_1_ON.rda', 'GSH_MEGA_1_OFF.rda'},{'GSH_MEGA_1_water.rda'});
    8. Siemens TWIX data (no water reference), run: MRS = GannetLoad({'GSH_MEGA_1_metab.dat'});
    9. Siemens TWIX data (with water reference), run: MRS = GannetLoad({'GSH_MEGA_1_metab.dat'}, {'GSH_MEGA_1_water.dat'});
  11. Then run GannetFit: MRS = GannetFit(MRS);

 

1. Mikkelsen M, Saleh MG, Near J, et al. Frequency and phase correction for multiplexed edited MRS of GABA and glutathione. Magn. Reson. Med. 2017;0:1–8. doi: 10.1002/mrm.27027.