MR Spectroscopy Analysis Tools

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. <>.


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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1.7.0 by Martin Wilson, 3 months ago

Report a bug at

Browse source code at

Authors: Martin Wilson [cre, aut] , Yong Wang [ctb] , John Muschelli [ctb]

Documentation:   PDF Manual  

GPL-3 license

Imports abind, plyr, foreach, pracma, stringr, complexplus, signal, matrixcalc, minpack.lm, nnls, utils, graphics, grDevices, smoother, readr, magrittr, ptw, viridisLite, mmand, RNifti, RNiftyReg, fields, MASS, shiny, miniUI, oro.dicom, numDeriv, nloptr, irlba, tibble, jsonlite

Suggests neurobase, oro.nifti, knitr, rmarkdown, testthat, doParallel

See at CRAN