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@markmikkelsen markmikkelsen released this 30 Jul 22:59
· 186 commits to main since this release
v3.2.0
522fabb

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
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