Gannet Beta version available through github

Gannet is now freely available through this link to github.Click on the GANNETMaster BETA Download.zip link. (This link allows me to log downloads).

Gannet:

• analyses GABA-edited MRS data saved as GE P-file, Philips .data or .sdat, or Siemens .rda.
• is designed for batch analysis of entire study datasets
• is matlab-based 
• saves pdf output showing each dataset.

This software is provided without warranty.

We are managing version control of the code through github which also allows downloads.  It may be possible to dowmload without signing in, but it might be worth getting an account if you intend to use Gannet, so you can watch the repository richardedden/GannetMASTER.


I will post soon about how to get started and will add some example data files.  The analysis code pulls a lot of information about acquisitions from the file headers, but some assumptions are made (based on our own defaults), for example about the ordering of OFF and ON within the data.

GABA phantom recipe

It seems that there is some value in a standardized GABA phantom for cross-platform testing etc... This recipe is also a reasonable place to start if you want a 'will-work-without-much-thought' option.  Everything is available form Sigma Aldrich.

• Container: 1 liter Nalgene bottle style 2125
• Buffer: One PBS sachet P5368
• GABA: 1.03 g (RMM 103.1) A2129 

Make up to 1 liter with deionized water.  pH can be adjusted using NaOH/HCl (but to a first approximation does not need to be).

Setting up a MEGA-PRESS scan with the Philips patch

***These instructions are no longer current 9/2014***

These instructions are intended to help anyone with our patch get things set up for GABA editing. They are Philips- and patch-specific.

1. Start with a short-TE PRESS scan
2. In Initial, increase the TE to 68 ms.
3. In Geometry, change the voxel size to ~3x3x3 cm^3.
4. In Contrast:
• Change Gradient mode to Maximum and PNS mode to high.
• Select MEGA basic in BASING pulse options.
• Pulse duration 14ms, freq1 7.46 ppm, freq2 1.9 ppm. [OFF first, edit 8/19/12]
5. In Motion, set phase cycles and averages to 8, startup acquisitions 0 and turn off frequency correction.
6. In Dyn/ang, Dynamic study individual, 40 dynamic scans.
7. In Postproc, turn off spectral correction.
8. Set up a separate non-water-suppressed PRESS scan for quantification relative to water.