`NEWS.md`

- Added glycerol simulation parameters, e.g. get_mol_paras(“glyc”).
- Bug fix for read_ima_* functions.
- Improved y = 0 baseline for stackplot when setting bl_lty parameter.
- Removed norm_mrs function and replaced with scale_spec for simple data scaling tasks, eg scaling based on the integration of a spectral region.
- Added spec_op function for performing simple summary operations on spectral segments.
- Changed the name of scale_mrs function to scale_mrs_amp.
- Added mean_mrs_list function.
- Improved LCM RAW and BASIS readers (contribution from Alex Craven).

- ABfit frequency shifts limits are now specified in ppm rather than Hz to improve consistency between field strengths.
- NAA linewidth is now estimated and output by ABfit when NAAG is absent - useful for BRAINO phantom scans.
- Warning now given when spectra are mathematically combined and are not both in the same time/frequency domain.
- sum_mrs function added to simplify combining spectra within a pipe.
- scale_mrs function added to simplify scaling a spectrum within a pipe.
- add_noise function added to simplify generating simulated data with a pipe.
- hsvd_filt function now accepts a frequency range in ppm units and gives the option to return the model rather than the filtered data.
- Bug fix for hsvd_filt function where the max_damp argument was ignored.
- SVS reference scans, found in some TWIX files, are now removed by default.
- Bug fix for reading list/data when only one coil element is used.

- Added 2HG and citrate simulation parameters. e.g. get_mol_paras(“2hg”).
- Better print output for molecular definitions.
- Added metabolite and basis simulation vignettes.
- Bug fix for setting the ppm reference when reading LCModel RAW files.
- Bug fix for ABfit CRLB calculation of combined signals, eg tNAA, tCr.

- Options added to allow extra information to attached to mrs_data and fit_result objects as a data frame.
- New functions (combine_fit_XXX) for working with multiple fit results contained within a list structure.
- Basis set and noise region are now checked for validity in ABfit.
- Added spant_abfit_benchmark function.
- Tentative functions for performing “standard” 1H brain analyses: svs_1h_brain_analysis and svs_1h_brain_batch_analysis.
- Improved support for LCModel analyses.

- Fix for NIfTI MRS reader/writer.
- ortho3 now shows correct labels for orientations other than RAS.
- ortho3_int function renamed to ortho3_inter.
- Argument order change to plot_voi_overlay and plot_voi_overlay_seg to be more consistent with ortho3.
- Regression fix for partial volume segmentation plotting.
- Echo time parameter is now stored in the meta structure.
- ABfit now performs a 1D phase parameter search before the prefit stage to improve reliability. May be disabled with the prefit_phase_search fit option.

- NIfTI MRS reader and writer now uses the header extension for metadata. Thanks to Jon Clayden for adding extension read/write support to the RNifti package.
- Default plots now have gridlines in the y-direction and the plot line is now thicker and coloured blue.
- Opacity option added to the plotting functions (alpha).
- Bug fix for comb_coils with SVS data.
- Bug fixes for Siemens geometry information.
- Changed the ordering of arguments to write_mrs and write_mrs_nifti to improve consistency with other functions.
- Internal function (ortho3) now used to plot voxel locations on MRI.
- Internal dicom reader function added.
- Tentative support for Siemens and Philips DICOM MRS format added.
- Internal changes to the way orientation information is handled.

- Added gridplot function.
- New functions added for down sampling.
- Added signal space projection method for MRSI.
- Geometry information is now read from Siemens twix files.
- GitHub actions are now used for continuous integration instead of Travis and AppVeyor.
- Added precomp function to avoid repeated computation.
- mrs_data2mat function now collapses all dimensions to dynamics by default.
- mrs_data objects now store the nucleus.
- Added a reader for old Varian format (fid/procpar) data.

- Added write_mrs function which guesses the output format from the file extension or can be specified as an argument. write_mrs_XXX functions have been depreciated.
- read_mrs function now tries to guess the format from the file extension.
- Added json sidecar to NIFTI MRS export function.
- Added the option to read MRS data from a NIFTI file and json sidecar using the read_mrs function.
- Changed default crop_spec region to between 4.0 and 0.2 ppm.

- Bug fix for GE P file reader.
- Added downsample_mrs function.
- Tentative function (write_mrs_nifti) to write MRS data as a NIFTI format file
- for evaluation purposes only.

- Added an option to ABfit to allow the metabolite amplitudes to be negative (ahat_calc_method).
- Removed lsei package dependency.

- Added the option to plot a y = 0 baseline trace for stackplot.mrs_data.
- Added convenience functions to read and write mrs_data to rds format.

- Added get_fit_table function to combine all fit tables in a fit_result object into a single dataframe.
- ppm function can now be applied to fit result objects.
- Bug fix for plot_slice_fit_inter and added the option to specify a denominator.
- Added the option to specify a denominator to plot_slice_fit.

- Added the option to display a progress bar in fit_mrs function for better conformance to “Writing R Extensions” in non-interactive use.
- Changed test tolerance to accommodate differences with OSX.

- Performance improvement for HSVD water filter.
- ABfit unit tests are now run on simulated data to improve consistency between different platforms.
- Improvements to fit amplitude scaling code.
- Improved checking for mrs_data processing functions.
- Added preprocessing steps vignette.

- Improved ppm labels for ABfit plot results.
- Bug fix for plot_slice_fit when using fits from masked data.
- Updated unit tests.
- Added vignette on manually adjusting ABfit baseline smoothness.
- Updated the introduction vignette.
- Bug fixes for image and stackplot functions for masked MRS data.
- Bug fix for using RATS with masked MRS data.
- Changes to prepare for for R 4.0.0.

- ABfit analysis method has been added, and is now default for the mrs_fit function.
- Added reader for LCModel RAW format data.
- Added read_mri_dyn_dir function for reading dynamic MRS exported from Siemens scanners.
- Bug fixes for 2D MRSI voxel segmentation calculation.
- Bug fixes for Siemens IMA format reader for SVS data.
- Optional colourbar added to ortho3 function.

- Added Asc, BHB, Cho, PEth and Ser simulation parameters.
- Added ker option to get_mrsi_voi function.
- Added append_basis function to combine two basis sets objects.
- The align function now accepts more than one reference frequency.

- Added a function to grid shift 2D MRSI data in the x/y direction.
- Better plotting/fitting support for masking data by setting data points to NA.
- Bug fix for interactive voxel selection position indicator.
- Added mask_xy to mask voxels in a centred rectangular region.
- Minor changes to improve parallel processing support.

- SNR is now defined as the max data point divided by the standard deviation of the noise (n.b. factor of two has been removed in-line with upcoming terminology paper).
- Default rats method improved to work with multidimensional datasets.
- Added norm_mrs function to normalise the intensity of spectral data.
- Added bc_constant function to correct spectral baselines by a constant offset.
- Added re_weighting function to apply a resolution enhancement weighting to the FID.
- Performance improvement for apodise_xy function.
- sd function now works for mrs_data.
- Added 2D MRSI support for Siemens IMA format.

- Bug fix for using auto_phase function with a single spectrum.
- Bug fix for comb_coils not returning unaveraged data when requested.
- Added options to combine metabolite signals from the stackplot of a fit object and adjust the plot margins.
- Added comb_fits function.
- Added collapse_to_dyns function for mrs_fit objects.
- RDA reader now extracts geometry information.

- Added options to omit basis signals, change label names and combine lipid and MM signals from the stackplot of a fit object.
- Added auto_phase function for zeroth order phase-correction of simple spectra.
- Added get_subset function to aid MRSI slicing.
- Added decimate_mrs function.
- Added fit_amps function to quickly extract amplitude estimates from a fit object.
- Bug fix for int_spec function.
- sim_basis function arguments updated to accept acq_par objects.

- Various bug fixes for Siemens TWIX reader.
- rats and tdsr functions now use the mean spectrum as the default reference.
- Added the option to remove the x axis in an mrs_data plot.
- Added ylim and y_scale options to fit plotting.
- Added %$% operator from magrittr package.
- Added an interpolation option to calc_spec_snr.
- Added hline and vline options to image.mrs_data.

- Fit results stackplot now has the option to display labels.
- Added the option to reverse eddy current correction.
- Improved GE p-file reader.
- diff function can now be applied to mrs_data objects.
- Complex functions: Re, Im, Mod, Arg and Conj can now be applied to mrs_data objects.
- Default simulations for Glc and NAAG have been improved.

- Added mar argument to plot command.
- td2fd and fd2td now give warnings when used with data already in the target domain.
- Improved documentation formatting consistency and fixed some spelling errors.
- Added rats method.

- The names of in-built pulse sequence functions now all start with seq_* to make them easier to find.
- Added new functions to simulate the following MRS sequences: CPMG, MEGA-PRESS, STEAM, sLASER. sLASER sequence kindly contributed by Pierre-Gilles Henry.
- Bug fix for get_mol_names function.
- stackplot function now accepts labels argument and time-domain plotting.
- def_acq_paras function now accepts arguments to override the defaults.
- Added a source field to mol.paras object to cite the origin of the values.
- Option to restore plotting par defaults.
- The magrittr pipe operator is now exported.

- Updated plotting modes to be one of : “re”, “im”, “mod” or “arg”.
- Updated int_spec function to use “re”, “im”, or “mod”.
- Added a function to replicate data across a particular dimension.
- Added a convenience function to simulate normal looking 1H brain MRS data.
- phase and shift functions now accept vector inputs.

- Added new function for frequency drift correction.
- Added support for Siemens ima and TWIX SVS data.
- Added support for GE p-file SVS data.
- Added apply_axes fn.
- Support for reading SPM style segmentation results (spm_pve2categorical).

- Interactive plotting function added for fit results - plot_fit_slice_inter.
- Bug fix for appending dynamic results.
- Bug fix for reading list data files without reference data.
- Bug fix for append_dyns function.
- basis2mrs_data function has been extended to allow the summation of basis elements and setting of individual amplitudes.
- Added a shift function for manual frequency shift adjustment.
- Added initial unit tests and automated coveralls checking.

- A default brain PRESS basis is now simulated by the fit_mrs function when the basis argument isn’t specified.
- Added calc_peak_info function for simple singlet analyses.
- crop_spec function now maintains the original frequency scale.
- The basis set used for analyses has now been added to the fit result object.
- Bug fix for simulating basis sets with one element.
- lb function can now be used with basis-set objects.
- Bug fix for spar_sdat reader for non-localised MRS.
- AppVeyor now being used to test Windows compatibility - John Muschelli.

- Bug fix for SPAR/SDAT SVS voxel dimensions.
- MRSI support added for Philips SPAR/SDAT data.
- Fit plots now default to the full spectral range unless xlim is specified.
- Fit plots allow the x, y, z, coil, dynamic indices to be specified.
- Added the option to subtract the baseline from fit plots.

- Added stackplot method for fit objects.
- Added functions for registering and visualising SVS volumes on images and performing partial volume correction.
- Philips “list data” also now reads noise scans.
- calc_coil_noise_cor, calc_coil_noise_sd functions added to aid coil combination.
- Documentation updates for plotting methods.
- Added some simulation methods to userland.

- Added Siemens RDA format reader.
- Added Philips “list data” format reader.
- Added Bruker paravision format reader.
- Added PROPACK option for HSVD based filtering.
- Added a coil combination function.
- Bug fix for incorrect ppm scale on fit plots when fs != 2000Hz.
- Bug fix for VARPRO analytical jacobian calculation.

Developed by Martin Wilson.

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