NEWS.md

In neuroconductor/spant: MR Spectroscopy Analysis Tools

spant 1.12.0

• 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

• 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

• 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

• 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

• 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

• 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

• 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

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

spant 1.4.0

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• First public release.

neuroconductor/spant documentation built on May 25, 2021, 1:49 a.m.