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TARQUIN Changelog

What's new in TARQUIN 4.3.10

Mar 3, 2017
  • Changes and fixes:
  • Residual water amplitude now listed in csv results output and expressed as a percentage of unsuppressed water signal in the PDF output (HSVD based water removal for SVS data only).
  • Bug fix to allow dyn freq correction to be applied with auto referencing set to false.
  • Add to c/l and GUI option to keep the pre water suppression shift (can be a useful alternative to "auto referencing" when the residual water signals are poorly suppressed).
  • Added internal basis set for metabs, excluding MM and Lipid signals.
  • Bug fix for k-space filtering of 2D MRSI with odd number of voxels in a given direction.

New in TARQUIN 4.3.8 (Jan 29, 2016)

  • New command line option to append pdf output with a stack plot (--stack_pdf true). A very useful contribution from Stephen Wastling at KCL.
  • New internal basis set including experimentally derived MM basis signal. May give more stable results for normal(ish) brain at 3T, TE~30ms.
  • Bug fix for Siemens IMA and RDA MRSI where the row and col voxel dimensions were the wrong way round. Thanks to Chris Adamson and Bhavana Solanky for helping with this.
  • Command line help corrected to list --crlb_optim.
  • MPRESS GABA basis set update to linewidth of GABA_A peak.
  • Internal basis for MEGA-PRESS peaks have been rescaled to 1.0.

New in TARQUIN 4.3.7 (Jan 29, 2016)

  • Regression fix where --para_file was not accepted as a valid command line options.
  • Bug fix for where dynamic WS scans didn't match W scans.
  • Improved command line parsing code to reduce the number of nested scopes to get round a limitation of the MSVS compiler.
  • Added a command line option to manually override the number of GE water reference data frames (--ge_wframes).
  • Improved p-file reading for GE MEGA-PRESS sequences.
  • Fixed metabolite FWHM estimate for MEGA-PRESS data.
  • Internal basis for MEGA-PRESS peaks have been rescaled to 0.4.
  • Added a command line option to make dynamic frequency correction act in a pairwise fashion ("--pdfc true"). May be useful for MEGA-PRESS).

New in TARQUIN 4.3.6 (Apr 18, 2015)

  • GUI bug fix where MRI slice changes caused a crash in some cases.
  • GUI bug fix for exporting gnuplot pdf fit of MRSI data
  • numbers now match the spectrum displayed.
  • Gnuplot output now sets %CRLBs to >999 where appropriate to avoid unnecessary large numbers and inf inconstancies between platforms.
  • Bug fix for x axis direction when using Gnuplot 5.x.
  • A pre-fit to optimise phi0 only is now performed before the full fit to improve rare cases where the optimiser gets stuck in a local minimum. Can be enabled/disabled with the --pre_fit_phase option.
  • Bug fix for selecting dynamic water scans with the --av_list option.
  • Default max initial shift is now 0.1 PPM, since sensible data is very rarely shifted further than this.
  • Siemens DICOM fix for explicit sequence lengths.
  • Phi0 max/min limits can be specified with the --max_phi0 option.
  • Internal basis set for braino phantom now has narrower peaks better suited to typical T2 values seen in solution.
  • Bug fix for unit tests.

New in TARQUIN 4.3.5 (Dec 29, 2014)

  • Changes and fixes:
  • Tentative support for DICOM, SPAR/SDAT, IMA and RDA formats for 3D MRSI.
  • Dynamics scans can now be filtered prior to averaging by specifying a csv file (--av_list). Useful for fMRS studies.
  • Bug fix for GUI where program crashes following fitting.
  • Bug fix for GE p-files Rdb reader rev : 14.3 and 16.0 where the offset to data was incorrect by one frame. This caused a crash at the reconstruction stage.
  • Internal basis set option for 'braino' phantoms has now been added.
  • Correction for chemical shift of Gln spin from 2.19 to 2.109.
  • Internal basis set option for 'brain + glth' has now been added
  • this is the new default basis set because Gly is not present in normal brain in significant levels.
  • Added metabolite FWHM linewidth estimate to pdf output for QC purposes.
  • Dafult Gnuplot font sizes are now correct for more recent versions of the package.
  • Improvements for reading Philips DICOM MRS.
  • Bug fix for where dynamic WS scans didn't match W scans.
  • Added c/l option to estimate CRLB noise level from the frequency domain (--crlb_td false).
  • Added gnuplot pdf export option to the GUI
  • only tested for Linux and OSX, Windows users will probably need to add gnuplot to the path or specify location with "--gnuplot".
  • Bug fix for exporting single voxel (dpt) from an MRSI data set.
  • Exporting single voxel water data from an MRSI data set is now possible in the GUI.
  • Added GUI options to export single voxel CSV results and fit from an MRSI data set.
  • Added a command line option to freq reference to a single specified peak frequency (--ref_freq).
  • Improved GUI defaults for displaying MRSI maps and added option to remove grid lines.

New in TARQUIN 4.3.4 (Aug 2, 2014)

  • FIDs can be truncated prior to pre-processing to remove unnecessary noisy data points
  • saving memory and disk space for large MRSI datasets (--trunc_pts).
  • Improvement to reduce memory use when exporting large csv fit data files.
  • Bug fix where Cit was included in the default basis set for the GUI.
  • Bug fix for GE p-files where the offset to data was incorrect for rdb_header_rev 24,20.
  • Thanks to Felix Raschke for pointing this out.
  • Modest SNR improvement for multi-channel GE SVS coil combination (now weighted by water amplitude where available). Thanks to Felix Raschke and Jamie Near for letting me know that this is a better approach than un-weighted combination.
  • Improvements to default MRI window level and window width parameters.
  • Improvements to SPAR/SDAT SVS and 2D MRSI display on MRI.
  • The number of components used in the HSVD water removal can now be specified (--hsvd_comps).

New in TARQUIN 4.3.2 (Jul 3, 2014)

  • Bug fix should improve MRSI water removal quality.

New in TARQUIN 4.2.10 (Jun 10, 2013)

  • A TARQUIN application bundle has been developed for Mac OS X, see the documentation for how to use the command-line version in OS X. Big thanks to Andreas Bartsch, Adrian Garcia and Paul Mullins for testing.
  • Basis set shifts and dampings are now exported in the CSV results file.
  • Dynamic frequency shifts are now exported in the CSV results file when correction is performed.
  • Regression fix where an odd number of dynamic FIDs could not be loaded.
  • Regression fix where jmrui txt files could not be loaded.
  • Crash fix for k-space zero-filling a non-square acquisition.
  • Better error handling for bad CSV basis files.
  • DICOM MRS Columns and Rows tags now take precedence over SpectroscopyAcuisitionColumns and SpectroscopyAcuisitionRows.
  • Once data has been successfully loaded in the gui, a new data set can not be loaded "over the top". This should prevent some crashes.
  • gnuplot_cex command line parameter added. For some reason font sizes are differed between gnuplot 4.4 and 4.6 so this option has been added. A character expansion (cex) of 2 looks good for version 4.6.