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schorschinho GannetLoad can now process Siemens TWIX data from acquisitions that w…
…ere broken down into blocks. The 'join' mode is activated by simply adding 'join' to the list of arguments passed on to GannetLoad. Example: If you want to join the files metab1.dat, metab2.dat, and metab3.dat together, run MRS_struct = GannetLoad({'metab1.dat','metab2.dat','metab3.dat'},'join'). If you want to include a water-unsuppressed acquisition water.dat, run MRS_struct = GannetLoad({'metab1.dat','metab2.dat','metab3.dat'},{'water.dat'},'join').
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priam Added support for PRIAM. New function to read Philips DATA/LIST. Chan… Mar 27, 2018
.DS_Store New function CoRegStandAlone.m to co-register and segment MRS data (n… Sep 19, 2018
.gitignore
AlignUsingCr.m
AlignUsingH2O.m
AlignUsingPeak.m
CalcNoise.m
CallSPM12segmentation.m
CallSPM8segmentation.m
DICOMDeIdentify.m
DICOMRead.m New function CoRegStandAlone.m to co-register and segment MRS data (n… Sep 19, 2018
ExportToCSV.m
FitChoCr.m Optimized some initial conditions in GannetFit; data is now scaled du… Oct 16, 2017
FitCr.m
FitPeaksByFrames2.m
FiveGaussModel.m
FourGaussModel.m
FreqPhaseShiftNest.m More modifications Jul 5, 2017
GABAGlxModel.m Major modifications to GannetFit.m Jul 3, 2017
GEDeIdentify.m
GERead.m
Gannet3_logo.png
GannetCoRegister.m
GannetDiscernDatatype.m
GannetFit.m
GannetFitPhantom.m
GannetLoad.m GannetLoad can now process Siemens TWIX data from acquisitions that w… Oct 15, 2018
GannetManual.pdf
GannetMask.m Updating Edden local changes... non-specific Jun 20, 2016
GannetMask_GE.m
GannetMask_Philips.m
GannetMask_SiemensRDA.m
GannetMask_SiemensTWIX.m
GannetPlotPrePostAlign.m
GannetPlotPrePostAlign2.m New plotting function Oct 4, 2017
GannetPreInitialise.m
GannetQuantify.m
GannetSegment.m
GaussModel.m Major modifications to GannetFit.m Jul 3, 2017
LorentzModel.m
PaperPlot.m Updates to PaperPlot.m. Apr 27, 2018
PhilipsDeIdentify.m
PhilipsRead.m
PhilipsRead_data.m
PhilipsRead_data_7T.m Added support for Philips 7T .data files Aug 24, 2018
README.md
SDATread.m
SDATreadMEGA.m Updated mapVBVD tools; renamed key functions to avoid overlap with FID-A Aug 30, 2018
SiemensDICOMRead.m
SiemensRead.m
SiemensTwixRead.m
SixGaussModel.m
SpecifyOnOffOrder.m Corrected ON/OFF order for GABA/Glx HERMES data acquired on Philips i… Sep 25, 2018
Spectral_Registration.m
Spectral_Registration_HERMES.m Added support for Philips 7T .data files Aug 24, 2018
TWIXDeIdentify.m
TwoLorentzModel.m More modifications Jul 5, 2017
VAXD_to_uint64le.m
VAXF_to_uint32le.m Updating Edden local changes... non-specific Jun 20, 2016
VAXG_to_uint64le.m
dicom_get_spectrum_siemens.m
dicom_move.m Added support for DICOM MRS files. Aug 30, 2017
dicom_open.m Added support for DICOM MRS files. Aug 30, 2017
freadVAXG.m
fwriteVAXD.m Updating Edden local changes... non-specific Jun 20, 2016
image_center.m Cosmetic changes across the board, especially with output figures. Si… Jan 18, 2018
loadRawKspace.m Added support for PRIAM. New function to read Philips DATA/LIST. Chan… Mar 27, 2018
mapVBVD_Gannet.m
phase_correction_fids.m Modified phase_correction_fids.m Jul 27, 2017
precommit_unixtime
read_dcm_header.m read_dcm_header.m can now process DICOM sLASER data. Jul 19, 2018
read_twix_hdr_Gannet.m Updated mapVBVD tools; renamed key functions to avoid overlap with FID-A Aug 30, 2018
readraw_Gannet.m
sort_nat.m
twix_map_obj_Gannet.m Updated mapVBVD tools; renamed key functions to avoid overlap with FID-A Aug 30, 2018
uint32le_to_VAXF.m
uint64le_to_VAXG.m Added freadVAXG, uint32le_to_VAXF and uint64le_to_VAXG to code Dec 10, 2013
voxel2world_space.m GannetCoRegister.m output now shows structural image slices in correc… Feb 21, 2018
waterremovalSVD.m
write_xxx.m

README.md

Gannet 3.0

Open-source, MATLAB-based software for automated data processing and quantification of edited magnetic resonance spectroscopy (MRS) data.

Visit our website for the latest news on Gannet and our developments in edited MRS methodology.

Getting Started

Prerequisites

Gannet runs in MATLAB (we recommend using the latest release if possible). Additionally, Gannet requires that the following MATLAB toolboxes are installed:

  • Image Processing
  • Optimization
  • Signal Processing
  • Statistics and Machine Learning

To run the voxel co-registration and structural image segmentation modules, SPM12 must be installed.

Installing

The simplest way to install Gannet 3.0 is to download the zipped master folder, unzip it and then move the Gannet3.0-master folder to your MATLAB directory. To add the folder to your search path, run the following line of code in the command window of MATLAB:

macOS

addpath(genpath('~/Documents/MATLAB/Gannet3.0-master'));

Alternatively, open the Set Path dialog box from the MATLAB menu, click 'Add with Subfolders', find the Gannet3.0-master folder and then select it. When done, press 'Save' to permanently save the Gannet folder to MATLAB's search path.

Built With

Bugs, Contributions, Queries

For bug reporting, contribution requests and/or queries, please contact us at: gabamrs@gmail.com

Versioning

Versioning is conducted on a module-specific basis using the style YYMMDD. That is, each Gannet module has its own release version. Major changes or addition of new functionalities are reflected in the version updates, while minor bug fixes are not.

Authors

  • Richard Edden (The Johns Hopkins University)
  • C. John Evans (Cardiff University)
  • Ashley Harris (University of Calgary)
  • Nicolaas Puts (The Johns Hopkins University)
  • Georg Oeltzschner (The Johns Hopkins University)
  • Muhammad Saleh (The Johns Hopkins University)
  • Mark Mikkelsen (The Johns Hopkins University)

License

This software is open-source and does not have a specific license, but should you publish material that made use of Gannet in some way please cite the following publications:

  • Edden RAE, Puts NAJ, Harris AD, Barker PB, Evans CJ. Gannet: A batch-processing tool for the quantitative analysis of gamma-aminobutyric acid-edited MR spectroscopy spectra. J. Magn. Reson. Imaging 2014;40:1445–1452. doi: 10.1002/jmri.24478
  • Harris AD, Puts NAJ, Edden RAE. Tissue correction for GABA-edited MRS: Considerations of voxel composition, tissue segmentation, and tissue relaxations. J. Magn. Reson. Imaging 2015;42:1431–1440. doi: 10.1002/jmri.24903 (if you report tissue-corrected, water-referenced measurements)

Acknowledgments

We wish to thank the following individuals for their contributions to the development of Gannet:

  • Ralph Noeske (GE Berlin)
  • Peter Barker (The Johns Hopkins University)
  • Robin de Graaf (Yale School of Medicine)