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
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.
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.