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<h1 class="title toc-ignore">Release notes</h1>
<h4 class="date">Last updated: May 07, 2024</h4>
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<p><br></p>
<p>This page lists the stable releases of Gannet since v3.1.3. All
releases can be found on GitHub
<a href="https://github.com/markmikkelsen/Gannet/releases" target="_blank">here</a>
and
<a href="https://github.com/richardedden/Gannet3.1/releases" target="_blank">here</a>.
The development version of Gannet can be found
<a href="https://github.com/markmikkelsen/Gannet/tree/dev" target="_blank">here</a>.
For a more comprehensive list of changes to the current main version,
see the commits logged on GitHub
<a href="https://github.com/markmikkelsen/Gannet/commits/main" target="_blank">here</a>.</p>
<div id="section" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.3.2<a href="#section" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2023-08-02</span></p>
<div id="major-changes" class="section level3 hasAnchor">
<h3 class="hasAnchor">Major changes<a href="#major-changes"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Rewrote <code>SiemensRead.m</code> to reduce code length</li>
</ul>
</div>
<div id="minor-changes" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Updated <code>DICOMRead.m</code>, including to support Siemens XA30
data</li>
<li>Updated <code>SpectralRegistrationHERMES.m</code>
<ul>
<li>SNR limit is now estimated as in
<code>RobustSpectralRegistration.m</code></li>
<li>Bug fix for indexing for output saved from maximum likelihood
estimation</li>
</ul></li>
<li>Updated <code>dicm2nii</code> to version 2023.03.16</li>
<li>Updated <code>export_fig</code> to v3.40</li>
<li>Added Gannet documentation website URL to error dialog box</li>
<li>Changed the way path names are printed in error dialog box</li>
<li>Turned off iteration limit warning in <code>FitChoCr.m</code></li>
<li>Updated <code>UpdateGannet.m</code> to ensure all sub-directories
are added to the search path after updating</li>
<li>Added issue templates (in <code>.github/ISSUE_TEMPLATE</code>) for
blank issues, bug reports, and feature requests</li>
<li>Refined alignment of text/logos in output figures
<ul>
<li>The units used for displaying textual results are now normalized to
fit to any subplot dimension</li>
<li>The textual results in the <code>GannetCoRegister</code>,
<code>GannetSegment</code>, <code>CoReg</code>, and <code>Seg</code>
output figures are now correctly centered</li>
</ul></li>
<li>The weighted signal averaging method used is now saved in the
structure output</li>
<li>The weighting factors calculated when applying weighted signal
averaging are also now saved in the output</li>
<li>Updated <code>SavePDF.m</code> such that when appending PDFs using
<code>export_fig</code>, the figure size will now be equivalent in
pixels on Windows and Mac systems</li>
<li>Updated <code>NIfTIMRSRead.m</code></li>
<li>Updated <code>README.md</code></li>
<li>Updated <code>GannetFitPhantom.m</code></li>
<li>Removed redundant global frequency shift in
<code>RobustSpectralRegistration.m</code></li>
<li>The z-standardized MSEs calculated in the spectral registration
subroutines are now saved in the structure output</li>
<li>Updated <code>GannetVersion.m</code> to also output version numbers
of Gannet modules</li>
<li>A warning is now printed when users process Siemens .rda data
encouraging them to instead use TWIX (.dat) data</li>
<li>Added support for GE P-file header revision 30
(<a href="https://github.com/markmikkelsen/Gannet/issues/28" target="_blank">#28</a>)</li>
<li>MANY COSMETIC CHANGES</li>
</ul>
</div>
<div id="bug-fixes" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Bug fix for special character <code>\</code> in Windows file path
names printed in the error dialog box</li>
<li>Fixed bug in <code>GannetMask_NIfTI.m</code> where the co-registered
MRS voxel was incorrectly flipped in the <code>GannetCoRegister</code>
output figure</li>
<li>Fixed bug in <code>GannetQuantify.m</code> where the alpha value was
incorrectly being printed multiple times when multiple were run in
batch</li>
<li>Added fix in <code>VersionCheck.m</code> so that when users have
limited or restricted internet access, an error is avoided
(<a href="https://github.com/markmikkelsen/Gannet/pull/27" target="_blank">#27</a>)
- thanks <a href="https://github.com/alexcraven" target="_blank"><span
class="citation">@alexcraven</span></a>!</li>
</ul>
</div>
</div>
<div id="section-1" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.3.1<a href="#section-1" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2023-03-14</span></p>
<div id="new-features" class="section level3 hasAnchor">
<h3 class="hasAnchor">New features<a href="#new-features"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Compressed NIfTI files (*.nii.gz) are now fully supported</li>
<li>Gannet now fully quantifies metabolite levels for Cr, Cho, and NAA
(estimated from the OFF spectrum)</li>
</ul>
</div>
<div id="major-changes-1" class="section level3 hasAnchor">
<h3 class="hasAnchor">Major changes<a href="#major-changes-1"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Moved local signal model functions out of <code>GannetFit.m</code>
and into their own files:
<ul>
<li><code>BaselineModel.m</code></li>
<li><code>CalcIU.m</code></li>
<li><code>DoubleGaussModel.m</code></li>
<li><code>EtOHModel.m</code></li>
<li><code>GABAGlxModel.m</code></li>
<li><code>GaussModel.m</code></li>
<li><code>LorentzGaussModel.m</code></li>
<li><code>LorentzGaussModelP.m</code></li>
</ul></li>
<li>Added <code>GetFullPath.m</code>; Gannet now will find the full path
of input files by default</li>
<li>Renamed some of the data-loading functions</li>
</ul>
</div>
<div id="minor-changes-1" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes-1"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Added a check in <code>GannetQuantify.m</code> for datasets without
water references; <code>GannetQuantify.m</code> will not run if no water
references are present</li>
<li>Added a check in <code>GannetCoRegister.m</code> to ensure all
structural image files can be found</li>
<li>Updated <code>export_fig</code> to v3.33</li>
<li>Updated <code>dicm2nii</code> to version 2023.03.08</li>
<li>Updated <code>LICENSE</code> and <code>README.md</code></li>
<li>Updated <code>ExportToCSV.m</code></li>
<li>Updated <code>CoRegStandAlone</code> functions</li>
<li>Replaced use of <code>1i</code> with <code>complex()</code></li>
<li>Removed unused variable <code>T1max</code></li>
<li>Removed unnecessary <code>ones()</code> parameter in
<code>LorentzModel.m</code> and <code>TwoLorentzModel.m</code></li>
<li>Philips *.spar file extension is no longer saved in the output
structure</li>
<li>Removed calculation of <code>df</code> in <code>GannetLoad.m</code>;
added <code>dt</code> in its place</li>
<li>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</li>
<li>Added new output structure attribute <code>nrows_water</code></li>
<li>Reordered structure subfields for metabolites in
<code>GannetFit.m</code> and <code>ExportToCSV.m</code></li>
<li>Shifted Gannet logo and version number in PDF outputs slightly to
the right</li>
<li>Alpha values are now included in exported CSV files</li>
<li>Replaced the Gannet logo with a PNG version</li>
<li>MANY COSMETIC CHANGES</li>
</ul>
</div>
<div id="bug-fixes-1" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes-1"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Added a check for letter case of *.dcm and *.ima files in
<code>DICOMRead.m</code> and <code>SiemensDICOMRead.m</code>
(<code>dir()</code> is case-sensitive in Linux)</li>
<li>Added a fix to avoid an error where MATLAB tried to close figures
following an unrelated internal error, but no figures were created</li>
<li>Fixed a bug in <code>NIfTIMRSRead.m</code> that led to an error if
the <code>Manufacturer</code> field is not found in the data file
header</li>
<li>If <code>export_fig.m</code> cannot be found on the search path and
<code>append</code> has been flagged in
<code>GannetPreInitialise.m</code>, it is made clear to the user that
PDFs will be saved separately</li>
<li>Fixed bugs in <code>AlignUsingH2O.m</code></li>
<li>Fixed a bug in <code>SiemensDICOMRead.m</code> where an error
occurred if <code>centerFreq</code> is not found in the data file
header</li>
</ul>
</div>
</div>
<div id="section-2" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.3.0<a href="#section-2" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2022-10-22</span></p>
<div id="new-features-1" class="section level3 hasAnchor">
<h3 class="hasAnchor">New features<a href="#new-features-1"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Added functionality to read NIfTI-MRS files
(<a href="https://onlinelibrary.wiley.com/doi/10.1002/mrm.29418" target="_blank">Clarke
et al., MRM, 2022</a>) (<code>NIfTIMRSRead.m</code>); includes
additional new function <code>GannetMask_NIfTI.m</code> for voxel
co-registration</li>
<li>Added support for Utah Siemens MEGA-PRESS sequence (DICOM
files)</li>
<li>Added support for CMRR PRESS data (DICOM files)</li>
<li>Added support for Siemens XA30 sequence as provided by JHU</li>
<li>Changed <code>README</code> to <code>README.md</code>, which now
includes badges</li>
</ul>
</div>
<div id="major-changes-2" class="section level3 hasAnchor">
<h3 class="hasAnchor">Major changes<a href="#major-changes-2"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Coil combination of GE, NIfTI-MRS, and Siemens TWIX files is now
performed using generalized least squares
(<a href="https://onlinelibrary.wiley.com/doi/10.1002/jmri.23941" target="_blank">An
et al., JMRI, 2013</a>); this approach has been shown to result in
optimal SNR and reduce spectral artifacts</li>
<li>The Gannet logo has been reverted to the original image of a
gannet</li>
</ul>
</div>
<div id="minor-changes-2" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes-2"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Added functionality for GE data in
<code>AlignSubSpectra_PreAlignRef.m</code></li>
<li>An error is presented if not enough inputs are given for any of the
Gannet modules</li>
<li>CoRegStandAlone outputs can be hidden if
<code>MRS_struct.p.hide</code> is set to <code>1</code> in
<code>CoRegStandAlone.m</code> (default is <code>0</code>)</li>
<li>If the user has no internet connection, <code>VersionCheck.m</code>
and <code>UpdateGannet.m</code> will not run</li>
<li>Updated dicm2nii to latest version (version 2022.09.15)</li>
<li>Updated mapVBVD functions to latest version
(<a href="https://github.com/pehses/mapVBVD" target="_blank">https://github.com/pehses/mapVBVD</a>)</li>
<li>Turned off warnings of iteration limits in
<code>SpectralRegistrationHERMES.m</code> and
<code>GannetFit.m</code></li>
<li>Many cosmetic changes in the code</li>
</ul>
</div>
<div id="bug-fixes-2" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes-2"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Fixed bug in error reporting in <code>GannetFit.m</code></li>
<li>CoRegStandAlone routines now parse version numbers from the main
modules properly</li>
<li>Variable <code>filesExist</code> in <code>GannetSegment.m</code> may
not populate; it is now pre-initialized as a precaution</li>
<li>Bug fix in <code>GannetMask_SiemensRDA.m</code></li>
<li>Bug fixes for reading DICOM files</li>
</ul>
</div>
</div>
<div id="section-3" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.2.1<a href="#section-3" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2022-06-07</span></p>
<div id="minor-changes-3" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes-3"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li><code>PhaseCorrection.m</code> now deals better with spectra that
have a non-zero baseline</li>
<li>SPM12 now outputs forward deformation field (needed for normalizing
voxel masks to MNI space)</li>
<li>Updated <code>export_fig</code> to v3.27</li>
<li><code>CoRegStandAlone.m</code> now exports a CSV file</li>
<li>Various cosmetic changes</li>
</ul>
</div>
<div id="bug-fixes-3" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes-3"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Fixed sub-spectra alignment for GE HERCULES data</li>
<li>Fixed bug in <code>CoRegStandAlone.m</code></li>
<li>Fixed bug in <code>read_dcm_header.m</code> (thanks to Meredith
Reid)</li>
</ul>
<p><br></p>
</div>
</div>
<div id="section-4" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.2.0<a href="#section-4" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2021-07-30</span></p>
<div id="new-features-2" class="section level3 hasAnchor">
<h3 class="hasAnchor">New features<a href="#new-features-2"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Added <code>GannetVersion.m</code>, <code>VersionCheck.m</code>, and
<code>UpdateGannet.m</code>; 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</li>
<li>Added <code>ToolboxCheck.m</code> to check for missing MATLAB
toolboxes needed to run Gannet</li>
<li>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)</li>
<li>Users can now choose to use weighted (the default) or conventional
signal averaging in <code>GannetPreInitialise.m</code> (outlier scans
are removed when using conventional averaging, as before)</li>
<li>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:<a href="https://dx.doi.org/10.1016/j.bbe.2015.06.002" target="_blank">10.1016/j.bbe.2015.06.002</a>
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
<code>SignalAveraging.m</code></li>
<li>Yair Altman’s
<a href="https://github.com/altmany/export_fig" target="_blank">export_fig
toolbox</a> 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
<code>GannetPreInitialise.m</code> to do this); this is very useful for
easy QA of lots of data; note that
<a href="https://www.ghostscript.com/" target="_blank">Ghostscript</a>
needs to be installed for the appending of PDFs to work (NB: macOS users
should use this
<a href="https://pages.uoregon.edu/koch/" target="_blank">version</a> or
use
<a href="https://formulae.brew.sh/formula/ghostscript" target="_blank">Homebrew</a>
to install Ghostscript)</li>
<li>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 <code>UpdateGannet.m</code> when
<code>VersionCheck.m</code> 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
<code>GannetPreInitialise.m</code>); 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</li>
<li>Added an option in <code>GannetPreInitialise.m</code> 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)</li>
<li><code>PaperPlot.m</code> now allows users to plot an exemplary voxel
mask co-registered to the respective structural image</li>
<li>Added <code>GannetMask_GE_nii.m</code>; GE users can now use NIfTI
images instead of DICOMs to co-register their MRS voxels to structural
images</li>
<li>Added the ability to trim datasets</li>
<li>Extended the ability to concatenate files, including over multiple
subjects</li>
<li>Added a flag in <code>GannetPreInitialise.m</code>
(<code>MRS_struct.p.hide</code>) to prevent output figures from
displaying (useful when processing a large batch of files)</li>
</ul>
</div>
<div id="major-changes-3" class="section level3 hasAnchor">
<h3 class="hasAnchor">Major changes<a href="#major-changes-3"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>The outdated manual PDF has been removed; up-to-date software
documentation will now be found online: <a
href="https://markmikkelsen.github.io/Gannet-docs/index.html"
class="uri">https://markmikkelsen.github.io/Gannet-docs/index.html</a></li>
<li>Gannet is now licensed under the BSD 3-Clause License</li>
<li>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</li>
<li>Removed <code>MRS_struct.p.ON_OFF_order</code> from
<code>GannetPreInitialise.m</code>; 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)</li>
<li>The exception to this change is phantom data, where users will still
need to specify the order of editing pulses</li>
</ul>
</div>
<div id="minor-changes-4" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes-4"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Datasets with differing number of averages can now be
batch-processed together</li>
<li>Turned off the progress bar displayed when loading Siemens TWIX data
to reduce loading time</li>
<li>Renamed some files for the sake of clarity and style; removed
obsolete <code>GannetMask.m</code></li>
<li>Signal averaging and subtraction are now done in the new function
<code>SignalAveraging.m</code></li>
<li>Various improvements to <code>RobustSpectralRegistration.m</code>
(formerly <code>Robust_Spectral_Registration.m</code>) for better
handling of data acquired using very strong water suppression</li>
<li>The assumed concentration of pure water in <code>GannetFit.m</code>
and <code>GannetFitPhantom.m</code> (PureWaterConc) has been changed
from 55 to 55.51 mol/kg; this puts it in line with the same constant
used in <code>GannetQuantify.m</code></li>
<li>Added edits from Ralph Noeske (GE Berlin) to <code>GERead.m</code>
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)</li>
<li>In <code>GERead.m</code> and <code>PhilipsRead_data.m</code>,
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</li>
<li>Some changes to <code>SiemensDICOMRead.m</code> and
<code>DICOMRead.m</code> for smarter handling of data files: for each
dataset, metabolite and water data files should be stored in separate
folders</li>
<li>Improved <code>ExportToCSV.m</code>; 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</li>
<li>Rewrote <code>DiscernDataType.m</code> (formerly
<code>GannetDiscernDatatype.m</code>)</li>
<li>Minor changes and improvements to <code>PaperPlot.m</code></li>
<li>Minor changes to <code>CoRegStandAlone.m</code> functions</li>
<li>Minor changes to <code>SignalFilter.m</code></li>
<li>Simplified <code>EddyCurrentCorrection.m</code> (formerly
<code>phase_correction_fids.m</code>)</li>
<li>Set up SPM12 for batch tissue segmentation only when tissue
segmentation has not already been run and do it only once in a
batch</li>
<li>AllFramesFT (for the last loaded dataset) is now also saved in
<code>MRS_struct.spec</code></li>
<li>When saving the <code>MRS_struct</code> 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)</li>
<li>Removed <code>MRS_struct.p.sdat</code> from
<code>GannetPreInitialise.m</code> and the corresponding code from
<code>GannetLoad.m</code> (this feature was never really used by users
afaik)</li>
<li>Improved global zero-order phasing in
<code>SpectralRegistrationHERMES.m</code></li>
<li>Many cosmetic/aesthetic changes
<ul>
<li>The module output figures now show information useful for reporting
acquisition parameters and results (in line with the
<a href="https://onlinelibrary.wiley.com/doi/10.1002/nbm.4484" target="_blank">MRSinMRS</a>
checklist)</li>
<li>Co-registered/segmented voxel masks displayed in GannetCoRegister,
GannetSegment, and GannetQuantify output figures are now shown in yellow
rather than grayscale</li>
<li>Smarter stacking of HERMES difference spectra in
<code>PlotPrePostAlign.m</code> and <code>PlotPrePostAlign2.m</code>
(formerly <code>GannetPlotPrePostAlign.m</code> and
<code>GannetPlotPrePostAlign2.m</code>)</li>
<li>The Gannet documentation website URL is printed at the bottom of
every output figure</li>
<li>Removed irrelevant messages from being printed in the command window
during the analysis pipeline, replacing them with more useful
messages</li>
<li>Minor rearranging of results text in GannetSegment and
GannetQuantify output figures</li>
<li>Slight change to the y-axis labels of the Cr frequency spectrogram
in the GannetLoad output figure</li>
<li>Better reordering of <code>MRS_struct.out</code> subfields created
in <code>GannetFit.m</code></li>
</ul></li>
</ul>
</div>
<div id="bug-fixes-4" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes-4"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Frequency and phase offset estimates are now tracked correctly and
saved when running any of the spectral registration-based alignment
methods</li>
<li>Removed old debugging conditional statement in
<code>TWIXDeIdentify.m</code></li>
<li>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</li>
<li>Added EtOH signal parameters to <code>GannetQuantify.m</code></li>
<li>In <code>SiemensTwixRead.m</code>, 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</li>
<li>Fixed an orientation problem in <code>GannetMask_GE.m</code></li>
<li>Removed unnecessary complex conjugate transpose during FFT of water
data in <code>GannetLoad.m</code></li>
<li>Turned off warnings about legacy number generator in
<code>RobustSpectralRegistration.m</code> (for when rng and randn are
run in <code>SignalFilter.m</code>) if they are already turned on</li>
</ul>
<p><br></p>
</div>
</div>
<div id="section-5" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.1.5<a href="#section-5" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2020-03-02</span></p>
<div id="new-features-3" class="section level3 hasAnchor">
<h3 class="hasAnchor">New features<a href="#new-features-3"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Smarter checking of incorrect settings in
<code>GannetPreInitialise.m</code> by <code>CheckTargets.m</code></li>
<li>Major changes to <code>GannetFitPhantom.m</code> to bring it more in
line with <code>GannetFit.m</code></li>
<li>Added support for CMRR MEGA-sLASER sequence in
<code>SiemensTwixRead.m</code></li>
<li>In <code>SubSpectralAlign.m</code>, if very strong water suppression
was used, use Cho instead of residual water to align subspectra of
GABA-, Lac-, and EtOH-edited datasets</li>
</ul>
</div>
<div id="minor-changes-5" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes-5"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Noise estimation in <code>CalcNoise.m</code>,
<code>Robust_Spectral_Registration.m</code>, and
<code>SignalFilter.m</code> is now performed between 8 and 10 ppm to
account for datasets that have shorter spectral widths</li>
<li>Cleaned up code in <code>GannetFit.m</code></li>
<li>Quantification of Lac now explicitly defined as Lac+MM</li>
<li>Improved functionality of <code>PaperPlot.m</code></li>
<li>In <code>SiemensTwixRead.m</code>, when a water reference is
present, coil sensitivity and phase is based on the point index that is
at the top of the echo, rather than simply fixing it to the first
point</li>
</ul>
</div>
<div id="bug-fixes-5" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes-5"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Minor bug fixes in CoRegStandAlone functions</li>
<li>Corrected use of random number generation in
<code>SignalFilter.m</code> when performing noise replacement to ensure
the same results are reproduced each time it is run on a dataset</li>
</ul>
<p><br></p>
</div>
</div>
<div id="section-6" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.1.4<a href="#section-6" class="anchor-section"
aria-label="Anchor link to header"></a></h2>