3.3.2

Major changes

• Rewrote SiemensRead.m to reduce code length

Minor changes

• Updated DICOMRead.m, including to support Siemens XA30 data
• Updated SpectralRegistrationHERMES.m
  • SNR limit is now estimated as in RobustSpectralRegistration.m
  • Bug fix for indexing for output saved from maximum likelihood estimation
• Updated dicm2nii to version 2023.03.16
• Updated export_fig to v3.40
• Added Gannet documentation website URL to error dialog box
• Changed the way path names are printed in error dialog box
• Turned off iteration limit warning in FitChoCr.m
• Updated UpdateGannet.m to ensure all sub-directories are added to the search path after updating
• Added issue templates (in .github/ISSUE_TEMPLATE) for blank issues, bug reports, and feature requests
• Refined alignment of text/logos in output figures
  • The units used for displaying textual results are now normalized to fit to any subplot dimension
  • The textual results in the GannetCoRegister, GannetSegment, CoReg, and Seg output figures are now correctly centered
• The weighted signal averaging method used is now saved in the structure output
• The weighting factors calculated when applying weighted signal averaging are also now saved in the output
• Updated SavePDF.m such that when appending PDFs using export_fig, the figure size will now be equivalent in pixels on Windows and Mac systems
• Updated NIfTIMRSRead.m
• Updated README.md
• Updated GannetFitPhantom.m
• Removed redundant global frequency shift in RobustSpectralRegistration.m
• The z-standardized MSEs calculated in the spectral registration subroutines are now saved in the structure output
• Updated GannetVersion.m to also output version numbers of Gannet modules
• A warning is now printed when users process Siemens .rda data encouraging them to instead use TWIX (.dat) data
• Added support for GE P-file header revision 30 (#28)
• MANY COSMETIC CHANGES

Bug fixes

• Bug fix for special character \ in Windows file path names printed in the error dialog box
• Fixed bug in GannetMask_NIfTI.m where the co-registered MRS voxel was incorrectly flipped in the GannetCoRegister output figure
• Fixed bug in GannetQuantify.m where the alpha value was incorrectly being printed multiple times when multiple were run in batch
• Added fix in VersionCheck.m so that when users have limited or restricted internet access, an error is avoided (#27) - thanks @alexcraven!

3.3.1

New features

• Compressed NIfTI files (*.nii.gz) are now fully supported
• Gannet now fully quantifies metabolite levels for Cr, Cho, and NAA (estimated from the OFF
  spectrum)

Major changes

• Moved local signal model functions out of GannetFit.m and into their own files:
  • BaselineModel.m
  • CalcIU.m
  • DoubleGaussModel.m
  • EtOHModel.m
  • GABAGlxModel.m
  • GaussModel.m
  • LorentzGaussModel.m
  • LorentzGaussModelP.m
• Added GetFullPath.m; Gannet now will find the full path of input files by default
• Renamed some of the data-loading functions

Minor changes

• Added a check in GannetQuantify.m for datasets without water references; GannetQuantify.m will
  not run if no water references are present
• Added a check in GannetCoRegister.m to ensure all structural image files can be found
• Updated export_fig to v3.33
• Updated dicm2nii to version 2023.03.08
• Updated LICENSE and README.md
• Updated ExportToCSV.m
• Updated CoRegStandAlone functions
• Replaced use of 1i with complex()
• Removed unused variable T1max
• Removed unnecessary ones() parameter in LorentzModel.m and TwoLorentzModel.m
• Philips *.spar file extension is no longer saved in the output structure
• Removed calculation of df in GannetLoad.m; added dt in its place
• Exported CSV files will no longer be overwritten if a CSV file of the same name already exists in
  the output directory; instead, a new file is created and appended with an integer
• Added new output structure attribute nrows_water
• Reordered structure subfields for metabolites in GannetFit.m and ExportToCSV.m
• Shifted Gannet logo and version number in PDF outputs slightly to the right
• Alpha values are now included in exported CSV files
• Replaced the Gannet logo with a PNG version
• MANY COSMETIC CHANGES

Bug fixes

• Added a check for letter case of *.dcm and *.ima files in DICOMRead.m and SiemensDICOMRead.m
  (dir() is case-sensitive in Linux)
• Added a fix to avoid an error where MATLAB tried to close figures following an unrelated internal
  error, but no figures were created
• Fixed a bug in NIfTIMRSRead.m that led to an error if the Manufacturer field is not found in
  the data file header
• If export_fig.m cannot be found on the search path and append has been flagged in
  GannetPreInitialise.m, it is made clear to the user that PDFs will be saved separately
• Fixed bugs in AlignUsingH2O.m
• Fixed a bug in SiemensDICOMRead.m where an error occurred if centerFreq is not found in the
  data file header

3.3.0

New features

• Added functionality to read NIfTI-MRS files (Clarke et al., MRM, 2022) (NIfTIMRSRead.m); includes additional new function GannetMask_NIfTI.m for voxel co-registration
• Added support for Utah Siemens MEGA-PRESS sequence (DICOM files)
• Added support for CMRR PRESS data (DICOM files)
• Added support for Siemens XA30 sequence as provided by JHU
• Changed README to README.md, which now includes badges

Major changes

• Coil combination of GE, NIfTI-MRS, and Siemens TWIX files is now performed using generalized least squares (An et al., JMRI, 2013); this approach has been shown to result in optimal SNR and reduce spectral artifacts
• The Gannet logo has been reverted to the original image of a gannet

Minor changes

• Added functionality for GE data in AlignSubSpectra_PreAlignRef.m
• An error is presented if not enough inputs are given for any of the Gannet modules
• CoRegStandAlone outputs can be hidden if MRS_struct.p.hide is set to 1 in CoRegStandAlone.m (default is 0)
• If the user has no internet connection, VersionCheck.m and UpdateGannet.m will not run
• Updated dicm2nii to latest version (version 2022.09.15)
• Updated mapVBVD functions to latest version (https://github.com/pehses/mapVBVD)
• Turned off warnings of iteration limits in SpectralRegistrationHERMES.m and GannetFit.m
• Many cosmetic changes in the code

Bug fixes

• Fixed bug in error reporting in GannetFit.m
• CoRegStandAlone routines now parse version numbers from the main modules properly
• Variable filesExist in GannetSegment.m may not populate; it is now pre-initialized as a precaution
• Bug fix in GannetMask_SiemensRDA.m
• Bug fixes for reading DICOM files

3.2.1

Minor changes

• PhaseCorrection.m now deals better with spectra that have a non-zero baseline
• SPM12 now outputs a forward deformation field (needed for normalizing voxel masks to MNI space)
• Updated export_fig to v3.27
• CoRegStandAlone.m now exports a CSV file
• Various cosmetic changes

Bug fixes

• Fixed sub-spectra alignment for GE HERCULES data
• Fixed bug in CoRegStandAlone.m
• Fixed bug in read_dcm_header.m (thanks to Meredith Reid)

3.2.0

New features

• Added GannetVersion.m, VersionCheck.m, and UpdateGannet.m; these new functions let users know the version of Gannet they have, if a newer release of Gannet is available, and will allow them to automatically update if wanted
• Added ToolboxCheck.m to check for missing MATLAB toolboxes needed to run Gannet
• Error dialog boxes are displayed at the end of the analysis pipeline if an error occurred (during a batch analysis, Gannet will skip to the next dataset and continue running)
• Users can now choose to use weighted (the default) or conventional signal averaging in GannetPreInitialise.m (outlier scans are removed when using conventional averaging, as before)
• Added a new (optional) method for robust, weighted signal averaging: weighted averaging by criterion function minimization (WACFM) using the generalized Cauchy distribution as the cost function; see doi: 10.1016/j.bbe.2015.06.002 for more details; additionally, instead of weighting difference pairs, the subspectra of each editing subexperiment are weighted to generate weighted subspectra, which are then subtracted; see SignalAveraging.m
• Yair Altman's export_fig toolbox is included as an optional toolbox that, if added to MATLAB's search path, Gannet will use to append all output PDFs from each module into a single PDF (a flag must be set in GannetPreInitialise.m to do this); this is very useful for easy QA of lots of data; note that Ghostscript needs to be installed for the appending of PDFs to work (NB: macOS users should use this version or use Homebrew to install Ghostscript)
• Implemented use of hyperlinks in info and error messages printed in the command window so that users can: (1) directly run a certain function (such as UpdateGannet.m when VersionCheck.m informs the user a new release is available); (2) go straight to the line of code where an encountered error can be fixed (such as errors in GannetPreInitialise.m); or (3) go to a website by clicking on the printed URL (such as to download SPM12); the relevant code has been borrowed from export_fig
• Added an option in GannetPreInitialise.m that allows users, when using robust spectral registration, to use the averaged pre-aligned subspectra as references for aligning the averaged post-aligned subspectra (this may be helpful when robust spectral registration makes the alignment of already good-quality pre-aligned spectra worse)
• PaperPlot.m now allows users to plot an exemplary voxel mask co-registered to the respective structural image
• Added GannetMask_GE_nii.m; GE users can now use NIfTI images instead of DICOMs to co-register their MRS voxels to structural images
• Added the ability to trim datasets
• Extended the ability to concatenate files, including over multiple subjects
• Added a flag in GannetPreInitialise.m (MRS_struct.p.hide) to prevent output figures from displaying (useful when processing a large batch of files)

Major changes

• The outdated manual PDF has been removed; up-to-date software documentation will now be found online: https://markmikkelsen.github.io/Gannet-docs/index.html
• Gannet is now licensed under the BSD 3-Clause License
• Alpha tissue correction is now performed on a by-metabolite basis rather than fixing the intrinsic WM:GM concentration to 1:2 (alpha) for all metabolites (assuming for now the ratio is 1:2 for GABA and Glx and 1:1 for GSH, EtOH and Lac); the alpha that is assumed is displayed in the GannetQuantify output figure
• Removed MRS_struct.p.ON_OFF_order from GannetPreInitialise.m; the order of editing pulses is now determined automatically; the relevant code has been borrowed from Osprey (this has only been tested to a limited extent so may require further tweaking)
  • The exception to this change is phantom data, where users will still need to specify the order of editing pulses

Minor changes

• Datasets with differing number of averages can now be batch-processed together
• Turned off the progress bar displayed when loading Siemens TWIX data to reduce loading time
• Renamed some files for the sake of clarity and style; removed obsolete GannetMask.m
• Signal averaging and subtraction are now done in the new function SignalAveraging.m
• Various improvements to RobustSpectralRegistration.m (formerly Robust_Spectral_Registration.m) for better handling of data acquired using very strong water suppression
• The assumed concentration of pure water in GannetFit.m and GannetFitPhantom.m (PureWaterConc) has been changed from 55 to 55.51 mol/kg; this puts it in line with the same constant used in GannetQuantify.m
• Added edits from Ralph Noeske (GE Berlin) to GERead.m for better handling of data when nechoes == 1; also changed the scaling factor if nechoes > 1 (hopefully this makes water-referenced measurements consistent across all data encoding flavors)
• In GERead.m and PhilipsRead_data.m, instead of using the first point in the FID for signal weighting, the most common point that is the max in the magnitude signal across all FIDs is now used
• Some changes to SiemensDICOMRead.m and DICOMRead.m for smarter handling of data files: for each dataset, metabolite and water data files should be stored in separate folders
• Improved ExportToCSV.m; a single .csv file is now exported for HERMES datasets; useful variables such as signal areas and Cr fit quality metrics are now also exported
• Rewrote DiscernDataType.m (formerly GannetDiscernDatatype.m)
• Minor changes and improvements to PaperPlot.m
• Minor changes to CoRegStandAlone.m functions
• Minor changes to SignalFilter.m
• Simplified EddyCurrentCorrection.m (formerly phase_correction_fids.m)
• Set up SPM12 for batch tissue segmentation only when tissue segmentation has not already been run and do it only once in a batch
• AllFramesFT (for the last loaded dataset) is now also saved in MRS_struct.spec
• When saving the MRS_struct structure, the .mat file is now saved using version 7.3 (for the rare case when the structure is >= 2 GB on 64-bit computers)
• Removed MRS_struct.p.sdat from GannetPreInitialise.m and the corresponding code from GannetLoad.m (this feature was never really used by users afaik)
• Improved global zero-order phasing in SpectralRegistrationHERMES.m
• Many cosmetic/aesthetic changes
  • The module output figures now show information useful for reporting acquisition parameters and results (in line with the MRSinMRS checklist)
  • Co-registered/segmented voxel masks displayed in GannetCoRegister, GannetSegment, and GannetQuantify output figures are now shown in yellow rather than grayscale
  • Smarter stacking of HERMES difference spectra in PlotPrePostAlign.m and PlotPrePostAlign2.m (formerly GannetPlotPrePostAlign.m and GannetPlotPrePostAlign2.m)
  • The Gannet documentation website URL is printed at the bottom of every output figure
  • Removed irrelevant messages from being printed in the command window during the analysis pipeline, replacing them with more useful messages
  • Minor rearranging of results text in GannetSegment and GannetQuantify output figures
  • Slight change to the y-axis labels of the Cr frequency spectrogram in the GannetLoad output figure
  • Better reordering of MRS_struct.out subfields created in GannetFit.m

Bug fixes

• Frequency and phase offset estimates are now tracked correctly and saved when running any of the spectral registration-based alignment methods
• Removed old debugging conditional statement in TWIXDeIdentify.m
• Explicitly specify color of water frequency trace in GannetLoad output figure as there appears to be a bug since MATLAB R2019b when using hold to overlay plots
• Added EtOH signal parameters to GannetQuantify.m
• In SiemensTwixRead.m, if no water reference is provided, use the most common point that is the max in the magnitude signal across all FIDs instead of just using the first point
• Fixed an orientation problem in GannetMask_GE.m
• Removed unnecessary complex conjugate transpose during FFT of water data in GannetLoad.m
• Turned off warnings about legacy number generator in RobustSpectralRegistration.m (for when rng and randn are run in SignalFilter.m) if they are already turned on