FSL-MRS Release History

This document contains the FSL-MRS release history in reverse chronological order.

1.1.9 (Tuesday 30th November 2021)

  • Fixed typos in fsl_mrs_proc help.

  • Fixed simulator bug for edited sequence coherence filters.

  • Modified API of syntheticFromBasis function.

  • Dynamic fitting now handles multiple different basis sets.

  • Fix mapped parameter uncertainties in dynamic MRS results.

  • Dynamic fitting results can now be saved to and loaded from a directory.

  • Added MH sample option to fsl_mrs, matches interactive python interface.

  • Changes to the dynamic fitting results API.

  • Allow tissue fractions with larger errors, but normalise. Error thrown if sum < 0.9.

  • Specialist phase & frequency alignment via dynamic fitting added.

  • Added fsl_mrs_preproc_edit as a script for preprocessing edited data.

  • Updated documentation with new install instructions.

  • Updated interactive fitting documentation

1.1.8 (Tuesday 5th October 2021)

  • Fix bug in fsl_mrsi when default MM are added to a incorrectly conjugated basis set.

  • Fix MRM reference in HTML report.

1.1.7 (Monday 4th October 2021)

  • Fixed commandline arguments for mrs_tools.

  • mrs_tools now handles files with passed without extension.

  • Fixed plotting orientation for preprocessing reports.

  • CRLB are now reported in scaled absolute and percentage units.

  • mrs_tools vis now handles DIM_COIL dimension appropriately with –display_dim command.

  • Added a –no_mean command to mrs_tools vis to remove the average signal in multi dimensional data.

1.1.6 (Monday 20th September 2021)

  • Updates to dynamic MRS fitting in prep for 2021 dwMRS workshop.

  • Dynamic MRS fitting beta: pending tests, documentation, and final features.

1.1.5 (Wednesday 11th August 2021)

  • Updated example MRSI data to conform to NIfTI-MRS standard.

  • Quantification will not fail if volume fractions do not sum exactly to 1.0 (to within 1E-3).

  • fixed bug in fsl_mrsi looking for TE in wrong header structure.

  • New mrs_tools command ‘conjugate’ to help fix NIfTI-MRS data with the wrong phase/frequency convention.

  • basis_tools remove has number of HLSVD components reduced to stop odd broad resonance behaviour.

  • fsl_mrs_proc align can now align across all higher dimension FIDs. Pass ‘all’ as dimension tag.

  • New command “fsl_mrs_proc model”. HSLVD modelling of peaks in defined region. Number of components settable.

  • Updates to basis set simulator. Non-uniform slice select gradients are now handled.

1.1.4 (Tuesday 3rd August 2021)

  • Fixed bug in calculation of molality concentration. Tissue mole fractions had been swapped for tissue volume fractions. Molar concentrations unaffected.

  • Fixed bug in mrs_tools split

  • Fixed bug in alignment of multi-dimensional data.

  • Fixed bug in fsl_mrsi: data without a water reference now works.

  • fsl_mrsi now outputs fitting nuisance parameters: phases, and shifts & linewidths for each metabolite group.

  • Add NIfTI-MRS reshape command

  • Add basis_tools remove_peak option to run HLSVD, typical usage for removing TMS peak.

  • Added an add_water_peak method to MRS class.

  • Updated fit_FSLModel defaults to match fsl_mrs command line defaults.

1.1.3 (Tuesday 29th June 2021)

  • Added mrs_tools script. Replaces mrs_vis and mrs_info. Adds split/merge/reorder functionality.

  • Added basis_tools script. Tools for manipulating (shifting, scaling, converting, differencing, conjugating, and adding to) basis sets.

  • Improved display of basis sets using mrs_tools or basis_tools.

  • Added ‘default’ MEGA-PRESS MM option to fsl_mrs and mrs class.

  • Preprocessing tools now add processing provenance information to NIfTI-MRS files.

  • Under the hood refactor of basis, MRS, and MRSI classes.

  • Updated density matrix simulator. Added some automatic testing.

  • Added documentation about the results_to_spectrum script.

1.1.2 (Friday 16th April 2021)

  • Added 2H information

  • Bug fixes

  • Added documentation around installation from conda

1.1.1 (Monday 15th March 2021)

  • SNR measurements should cope with negative peak amplitudes correctly

  • New metabolites added to list of default water referencing metabolites (Cr, PCr and NAA)

  • Quantification now takes into account T1 relaxation

  • Quantification module now fits the water reference FID to deal with corruption of first FID points.

  • Added plot in report to clarify referencing signals.

  • Restructure of internal quantification code.

1.1.0 (Thursday 18th February 2021)

  • Support for NIfTI-MRS format.

  • Preprocessing scripts reoriented around NIfTI-MRS framework

  • New script results_to_spectrum for generating full fits in NIfTI-MRS format from fsl_mrs results.

  • Documentation and example data updated for move to NIfTI-MRS.

  • Added mrs_info command to give quick text summary of NIfTI-MRS file contents.

  • Updates to the WIP dynamic fitting module.

1.0.6 (Tuesday 12th January 2021)

  • Internal changes to core MRS class.

  • New plotting functions added, utility functions for plotting added to MRS class.

  • fsl_mrs/aux folder renamed for Windows compatibility.

  • Moved online documentation to open.win.ox.ac.uk/pages/fsl/fsl_mrs/.

  • Fixed small bugs in preprocessing display.

  • Synthetic spectra now use fitting model directly.

  • Bug fixes in the fsl_Mrs commandline interface. Thanks to Alex Craig-Craven.

  • WIP: Dynamic fitting model and dynamic experiment simulation.

  • spec2nii requirement pinned to 0.2.11 during NIfTI-MRS development.

1.0.5 (Friday 9th October 2020)

  • Extended documentation of hardcoded constants, including MCMC priors.

  • Extended documentation of synthetic macromolecules.

  • Added flag to MCMC optimise baseline parameters.

1.0.4 (Friday 14th August 2020)

  • Fixed bug in automatic conjugation facility of fsl_mrs_preproc

  • jmrui text file reader now handles files with both FID and spectra

1.0.3 (Friday 10th July 2020)

  • Changed to pure python version of HLSVDPRO (hlsvdpropy). Slight speed penalty but hopefully reduced cross-compilation issues.

  • fsl_mrs_preproc now outputs zipped NIFTI files to match the rest of the command-line scripts.

  • Apodisation option added to alignment in fsl_mrs_proc and fsl_mrs_preproc. Reduces effect of noise. Default value is 10 Hz of exponential apodisation.

  • Fixed phasing subcommand added to fsl_mrs_proc allowing the user to apply a fixed 0th and 1st order phase.

  • mrs_vis now handles folders as an input for MRS data (still handles folders of basis files).

  • Conjugation command added to fsl_mrs_proc.

  • fsl_mrs_preproc automatically conjugates input spectra if required.

  • Typos and small bug fixes.

  • Documentation expanded.

1.0.2 (Saturday 27th June 2020)

  • Add missing requirement (pillow)

1.0.1 (Friday 19th June 2020)

  • Output folder in fsl_mrs_proc will now be created if it does not exist.

  • fsl_mrs_proc now handles data with a singleton coil dimension correctly.

  • –ind_scale and –disable_MH_priors options added to fsl_mrs and fsl_mrsi.

1.0.0 (Wednesday 17th June 2020)

  • First public release of package.