Gannet

Gannet

Gannet is a software package designed for the batch analysis of edited magnetic resonance spectroscopy (MRS) data. 

Gannet runs in Matlab, and is distributed as code rather than executables, empowering users to make local changes.  

Gannet is designed to run without user intervention, to remove operator variance from the quantification of edited MRS data.

Publication | Download | Past Versions | Documentation

Key Functions

  • GannetLoad processes time-domain MRS data;

  • GannetCoRegister generates a mask of the MRS voxel in T1-image space;

  • GannetFit models the edited spectrum;

  • GannetSegment derives gray matter, white matter and CSF voxel fractions;

  • GannetQuantify calculates tissue-corrected GABA levels.

The Gannet Team

Richard Edden

Richard Edden  

Professor of Radiology, The Johns Hopkins University School of Medicine

 Faculty Profile

 

Ashley Harris

Ashley Harris

Assistant Professor of Radiology, University of Calgary

Faculty Profile 

 

 

John Evans

John Evans

MRI Research Fellow, Cardiff University Brain Research Imaging Centre

Faculty Profile

Nicolaas Puts

Nicolaas Puts

Senior Lecturer of Forensic & Neurodevelopmental Sciences, King’s College London

Faculty Profile | Website

Georg Oeltzschner

Assistant Professor of Radiology, The Johns Hopkins University School of Medicine

Faculty Profile | Website

 

Mark Mikkelsen

Assistant Professor of Neuroimaging in Radiology, Weill Cornell Medical College

Faculty Profile

Muhammad G. Saleh

Research Associate of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine

Faculty Profile

Kimberly Chan

Instructor of Advanced Imaging Research Center and Psychiatry, UT Southwestern Medical Center

Faculty Profile

Examples

BlogExamples
GannetLoad

A. The plot top left shows the processed GABA-edited difference spectrum, the key output of the GannetLoad module. This plot shows the spectrum before frequency and phase correction above in green and the spectrum after frequency and phase correction…

Screen Shot 2015-12-31 at 9.35.49 AM.png
GannetFit

A. The plot top left shows the modeling of the GABA signal. The GABA-edited spectrum is shown in blue (across a more limited ppm range than in the GannetLoad output). Overlaid in red is the model of best fit (using a simple Gaussian model by default)…

Screen Shot 2015-12-31 at 9.44.31 AM.png
GannetCoRegister

GannetCoRegister takes location and orientation information from the headers of MRI and image data, and generates a binary mask representing the voxel location in the matrix of the image.  This is then visualized in three planes.

BlogExamples
Screen Shot 2015-12-31 at 9.52.21 AM.png
GannetSegment

GannetSegment calls an SPM segmentation of the T1-weighted anatomical image, and reports the tissue fractions of the voxel mask generated by GannetCoRegister.  If the segmentation has already been run, the prior output files will be used instead…

Screen Shot 2015-12-31 at 9.56.38 AM.png
GannetQuantify

GannetQuantify is the final step, combining modeled peak areas from GannetFit and voxel tissue fractions from GannetSegment with preset values for GABA and water relaxation and visibility, to deliver concentration values. Currently several values are…

Screen Shot 2018-12-14 at 1.36.20 PM.jpg
The Commonest Error

The single commonest error in Gannet arises from mis-setting the switches onofforder or WaterPositive in GannetPreinitialise.m. These switches correspond respectively to whether the first average is an edit-ON or edit-OFF average, and whether the res...