NEWS

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spant 3.1.0 (2024-12-17)

• Tentative implementation of a standard single voxel MRS processing pipeline function: fit_svs.
• spant user guide has been added to the project: https://spantdoc.wilsonlab.co.uk/
• Implemented basis caching for sim_basis.
• scale_amp_molar function has been depreciated. Please use scale_amp_legacy for LCModel style concentration scaling instead.
• Assumed T1 and T2 relaxation values for molal concentration scaling have been updated. See the user guide for details.

spant 2.24.0 (2024-11-14)

• Added argument to adjust the legend font size in ortho3 function.
• Improved metabolite simulation performance thanks to the expm package recently adding support for complex matrices.

spant 2.23.0 (2024-08-27)

• abfit options for lipid and MM maximum broadening and maximum frequency shift now default to be the same as the metabolite values unless explicitly changed.
• Added function to calculate the correlation matrix from a basis_set.
• Fix for RDA files where a comma is sometimes used as a decimal point.

spant 2.22.0 (2024-07-11)

• Added find_bids_mrs and mrs_data2bids helper functions.
• Improved handling of CMRR semi-LASER SVS water reference scans.
• Added functions for GLS coil combination.

spant 2.21.0 (2024-05-30)

• Fixed compiler warnings for Fortran code.
• Added glm_spec function.
• Added add_noise_spec_snr function.

spant 2.20.0 (2024-05-01)

• Added vertical line colour and linetype options for stackplots.
• Added option to give Y axis labels in units of seconds for spectrograms.

spant 2.19.0 (2024-03-22)

• Removed dependency on smoother package.
• Added functions for generating BOLD and trapezoidal response shapes.

spant 2.18.0 (2024-02-23)

• Improved automated file type detection.
• Bug fixes for DICOM MRS reader.
• scale_spec function now works with basis set objects.
• Added invert_fit option to plotting methods.

spant 2.17.0 (2023-11-28)

• Simulation duration output is now rounded to 2dp.
• sim_basis now accepts a character vector of molecular names.
• Added get_1h_brain_basis_names function.

spant 2.16.0 (2023-10-23)

• Added subset option to mean_dyns function.
• Added vline option to plot.
• Added common 31P brain metabolites.
• Added verbose option to sim_basis.

spant 2.15.0 (2023-09-14)

• An SNR estimate of zero in comb_coils is now a failure case.
• Bug fix for GE pfile reader header revision 20.
• Added a function for finding valid MRS files : find_mrs_files.

spant 2.14.0 (2023-07-19)

• Added vline argument to stackplot function.
• Added functions to set MRS data TR and number of transients.

spant 2.13.0 (2023-06-26)

• Improved defaults for sim_brain_1h function.
• Added scale_basis_amp function.
• Added crop_basis function.

spant 2.12.0 (2023-05-22)

• Amplitude scaling functions duplicate water reference amplitudes when sensible.
• Added hline option to the mrs_data plot function.

spant 2.11.0 (2023-04-22)

• Bug fix for Siemens RDA slice thickness detection.
• ProtocolName is now read from GE p-files.

spant 2.10.0 (2023-03-20)

• Tentative support for UIH DICOM MRS format.
• Improved support for reading GE p-files.
• Added a WIP function to export a one-page summary pdf of the fit result "one_page_pdf".

spant 2.9.0 (2023-03-03)

• Bug fix when using align function with masked data.
• mean_dyn_blocks returns the input data when block_size is set to 1.

spant 2.7.0 (2023-01-28)

• Added Manufacturer tag to metadata.
• Added mask_xy_corners and mask_xy_ellipse functions.
• Added functions to fit T1 and T2 relaxation curves.
• Updated CI checks.

spant 2.6.0 (2023-01-06)

• Masked spectra plotted with image are now shown with a value of zero.
• Added function to read .pta files - read_pulse_pta.
• Added a function to make basis set objects from a directory of LCModel formatted RAW files - make_basis_from_raw.
• Added horizontal line to fit result plots.
• Improvements to reading LCM .raw files with variable numerical columns.

spant 2.5.0 (2022-12-06)

• Improved function documentation for water concentration scaling.
• Added water and tCr scaling examples to the introduction vignette.
• Better error checking for reading ima files.
• read_basis function improved to work with variable formatting.
• Improved default method of time-domain signal amplitude estimation.
• Added helper functions for working with basis set objects: scale_basis_from_singlet, resample_basis and get_basis_subset.
• Bug fix for STEAM basis simulation being incorrectly scaled for internal water scaling methods.

spant 2.4.0 (2022-11-07)

• Performance improvement for reading VD format TWIX files.
• Function added to scale all metabolite levels by a set value (scale_amp_ratio_value).

spant 2.3.0 (2022-10-12)

• Verbose option added to read_ima_coil_dir and read_ima_dyn_dir functions.
• Support added for reading jMRUI txt formatted MRS data.
• sim_brain_1h default sequence changed to semi-LASER and line-broadening option added.
• Bug fix for reading LCModel RAW files.
• Bug fix for HSVD filter when only 0 or 1 components are found in the filter region.
• Improved removal of unwanted data points for reading TWIX formatted data.
• A json sidecar is automatically written when exporting NIfTI MRS formatted data.
• TWIX reader improved to only read data points from the last scan in the file. This also fixes a rare bug.

spant 2.2.0 (2022-09-08)

• peak_info function now works with masked datasets.
• Bug fix for HSVD function not working with frequency domain data.
• Bug fix for TWIX affine calculation when not using power of two matrix dimensions.
• New function (crop_td_pts_pot) to round a dataset length down to the nearest power of 2.
• Added ret_metab_only option to comb_coils.
• rats now only returns the corrected data by default, note this could break old code.

spant 2.1.0 (2022-07-21)

• y-axis label can now be changed with a new argument (yaxis_lab) to plot.mrs_data.
• Segmentation files are now checked for non-integer values.
• gridplot has better row and col number defaults for MRSI, and has a bug fix for plotting masked spectra.
• Updated functions for dealing with lists of MRSI datasets.
• Bug fix for crop_xy function when working with odd matrix sizes.

spant 2.0.0 (2022-06-22)

• magrittr pipe (%>%) is no longer loaded together with spant now the base pipe is part of R. Vignettes and tests have been updated to use the base pipe.
• NIfTI MRS writer no longer fails when dealing with a NULL affine matrix.
• Bug fix for NIfTI MRS writer, where frequency domain data was not correctly converted to time-domain before export.

spant 1.22.0 (2022-05-27)

• Added MSM and acetone to the set of internally defined molecules.
• write_mrs_nifti function removed from userspace. write_mrs should be used instead.
• set_td_pts and crop_td_pts now work with lists of spectra.
• Multiple files can now be written by passing a list of spectra to write_mrs.

spant 1.21.0 (2022-05-03)

• Bug fix for get_mrsi_voi function due to incorrect rounding of MRSI matrix dimensions in some cases.
• Added mask_fit_res function.
• Option added to get_2d_psf function to ensure odd output dimensions.
• Bug fix for using rats on datasets with masked voxels.
• Added spec_decomp function.
• Added ret_scale_factor option to scale_spec function.

spant 1.20.0 (2022-03-30)

• Options added to ft_dyns to return the modulus of the 2D spectra and to pre-transform the chemical shift axis if needed.
• Bug fix for printing lists of mrs_data objects.
• comb_coils function now supports lists of mrs_data objects.
• IMA reader now respects the verbose option in read_mrs.
• Bug fix for get_mrsi_voi ignoring the ker argument.
• Bug fix for reading Siemens TWIX files.

spant 1.19.0 (2022-02-14)

• Added sum_mrs_list function.
• Bug fix for operating on mrs_data with single values that aren't numeric types. For example, multiplying mrs_data by a single complex number now works.
• A number of common preprocessing functions now operate on lists of mrs_data objects.
• Change to NIfTI MRS reader to fix a failing test when using the development version of RNifti.

spant 1.18.0 (2022-02-08)

• Better behaviour when using stackplot with single spectra datasets.
• Better behaviour when using image with single spectra datasets.
• Bug fix for reading MEGA-PRESS data in TWIX format.
• Better error checking for lists of spectra.
• Bug fix for calculating NAA linewidth from MEGA-PRESS data.

spant 1.17.0 (2022-01-07)

• New function added (recon_twix_2d) for reconstructing basic phase encoded twix 2D MRSI data.
• File name argument for read_mrs now permits globbing, eg read_mrs("*.dcm").
• Improved plotting of metabolite maps containing infinite values.
• Improvements to GE p-file reader.
• Bug fix for TWIX MRSI voxel dimensions.
• get_mrsi2d_seg now returns partial volume maps as well as a data frame.
• Improved error handling for spec_op function.
• apodise_xy can now be applied to multi-coil and dynamic datasets.

spant 1.16.0 (2021-11-18)

• The package has been published in the Journal for Open Source Software : "spant: An R package for magnetic resonance spectroscopy analysis. JOSS 2021, 6(67), 3646".
• The basis result of the HSVD function is now an mrs_data object.
• The complete model signal is now output by the HSVD function.
• image function x-axis updated to be consistent with other plotting methods.
• Minor refactor of the simulation code and a dependency swap from complexplus to exmp packages.

spant 1.15.0 (2021-10-22)

• Added a unit test for reading and writing LCM .basis formatted files.
• Added FWHM estimates for tCr and tCho in ABfit.
• Added water suppression efficiency and water FWHM measures to the diagnostic output of svs_1h_brain_analysis.
• Added get_head_dyns and get_tail_dyns to return the first and last dynamic scans within a dataset.
• Fixed CI errors.
• Improved installation instructions.
• Removed comb_csv_results function and reduced the number of required packages.

spant 1.14.0 (2021-07-23)

• 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).

spant 1.13.0 (2021-06-09)

• 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.

spant 1.12.0 (2021-05-05)

• 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.

spant 1.11.0 (2021-03-28)

• 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.

spant 1.10.0 (2021-01-06)

• 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.

spant 1.9.0 (2020-12-15)

• 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.

spant 1.8.0 (2020-11-18)

• 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.

spant 1.7.0 (2020-07-09)

• 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.

spant 1.6.0 (2020-06-05)

• 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.

spant 1.5.0 (2020-05-11)

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

spant 1.4.0 (2020-04-20)

• 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.

spant 1.3.0 (2020-04-03)

• 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.

spant 1.2.1 (2020-03-15)

• 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.

spant 1.2.0 (2020-03-11)

• 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.

spant 1.1.0 (2020-03-01)

• 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.

spant 1.0.0 (2020-02-17)

• 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.

spant 0.19.0 (2019-12-06)

• 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.

spant 0.17.0

• 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.

spant 0.16.0 (2019-10-30)

• 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.

spant 0.15.0 (2019-09-19)

• 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.

spant 0.14.0 (2019-05-28)

• 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.

spant 0.13.0 (2019-04-25)

• 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.

spant 0.12.0 (2018-11-05)

• 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.

spant 0.11.0 (2018-07-20)

• 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.

spant 0.10.0 (2018-06-25)

• 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.

spant 0.9.0 (2018-03-07)

• 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.

spant 0.7.0 (2018-01-31)

• 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).

spant 0.6.0 (2017-10-25)

• 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.

spant 0.5.0 (2017-10-10)

• 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.

spant 0.4.0 (2017-08-09)

• 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.

spant 0.3.0 (2017-06-20)

• 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.

spant 0.2.0 (2017-05-24)

• 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.

spant 0.1.0 (2017-04-26)

• First public release.