MR Spectroscopy Analysis Tools

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) and spectral alignment: Wilson (2018) .


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.

Reference manual

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