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CHANGELOG.md

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This document contains the Spec2nii release history in reverse chronological order.

0.8.5 (Thursday 31st October 2024)

  • Add special case handling for DICOM dkd_svs_mslaser_msspnav sequence
  • More GE HBCD sequence adjustments.
  • Python 3.13 compatibility and testing, scipy dependency now >=1.13

0.8.4 (Monday 23rd September 2024)

  • GE HBCD sequence adjustments.

0.8.3 (Tuesday 9th August 2024)

  • Fix for multiple GE HBCD sequence names (again).

0.8.2 (Tuesday 9th July 2024)

  • Fix for multiple GE HBCD sequence names.

0.8.1 (Wednesday 3rd July 2024)

  • Bug fix for GE HBCD sequence.

0.8.0 (Wednesday 3rd July 2024)

  • Dropped support for Python 3.8 (EOL imminent), added support and testing for 3.12.
  • Compatibility with Numpy 2.0

0.7.4 (Thursday 18th April 2024)

  • Refinements and improvements to the GE SVS pipeline from Mark Mikkelsen.
  • Add support for older jMRUI text formats which have a slightly different syntax. With thanks to Donnie Cameron.
  • Handle odd case of XA like .twix headers in a VX baseline scan
  • Improved (and validated) handling of Dinesh Deelchand's slaser sequences with integrated references (svs_slaser(voi)_dkd(2))

0.7.3 (Tuesday 12th March 2024)

  • Siemens .rda format now had corrected and validated orientations (tested on VE11 baseline).
  • Siemens .rda format now handles MRSI/CSI data and matches DICOM output. Validated on VE11 baseline data.
  • Fixes in Siemens Twix special case for universal editing sequence (HERMES conditions).
  • Added handling of custom Bruker sequences mt_sLASER, mt_MEGA_sLASER_V35 and cl_STELASER_PA360_b.
  • Philips vendor MEGA-PRESS handled through DICOM pathway. Thanks to Sandeep Ganji and Yansong Zhao for their help.

0.7.2 (Thursday 7th December 2023)

  • SpectralWidth now added to header extension automatically to match bids specification.
  • NIfTI-MRS V0.8 now generated.
  • Better handling of philips spar/sdat tags and singleton dimensions.
  • Fixed bug where no name was set when a mixed folder of imaging and spectroscopy dicom was provided.

0.7.1 (Tuesday 7th November 2023)

  • The --anon flag can be passed with any call to anonymise after writing files.
  • The Siemens enhanced dicom filetype pathway now handles CSI data.
  • Fixed issue with RDA files having latin1 encoding. Thanks to gaunab on github. Fixes Issue #96.
  • Now support GE p-files up to version 30.0.

0.7.0 (Saturday 5th August 2023)

  • Fixed a bug in Philips Classic DICOM orientations (supplementing the fixes to Enhanced DICOM in 0.6.11)
  • Updated Hyper sequence special case for Siemens twix and GE.

0.6.11 (Friday 28th July 2023)

  • Fixed a bug in Philips spar/sdat orientations - this will affect voxels with rotations in more than one axes.
  • Fixed a bug in Philips DICOM orientations - this will affect voxels with rotations in more than one axes.
  • Python 3.7 now in end of life status and is no longer supported.
  • spec2nii dump/extract/insert can now be used to inspect and fix non-compliant NIfTI-MRS files.

0.6.10 (Monday 10th July 2023)

  • Stop tests being vendored as a top-level package. Bug introduced in 0.6.9.

0.6.9 (Friday 7th July 2023)

  • Add handling for the fidall sequence in GE.
  • Add handling for the slaser sequence in GE.
  • Update to nifti-mrs-tools 1.0.0 API.
  • Minor code fixes contributed by the community.

0.6.8 (Wednesday 22nd March 2023)

  • Added handling for the GE jpress sequence (for JH HURCULES sequence)
  • Added twix handling of the HYPER (smm_svs_herc_hyper) sequence (added by Aaron Gudmundson)
  • Better handling of partial acquisitions of Siemens and Philips HYPER sequence.

0.6.7 (Wednesday 15th March 2023)

  • spec2nii insert can now insert a compliant header object into a non-compliant NIfTI file to generate a new NIfTI-MRS file.
  • spec2nii insert can now update dwelltime using the optional --dwelltime argument.

0.6.6 (Thursday 9th March 2023)

  • Added in ability to generate empty NIfTI-MRS for twix-pathway MRSI scans.

0.6.5 (Wednesday 8th February 2023)

  • Fixed bug in philips and rda metadata translation functions.

0.6.4 (Tuesday 7th February 2023)

  • Added first pass at new spec2nii auto feature with automatic conversion for some formats.

0.6.3 (Monday 6th February 2023)

  • Added handling for GE presscsi and probe-s sequences.

0.6.2 (Sunday 5th February 2023)

  • Handle HYPER references in SPAR/SDAT pipeline
  • Handle HURCULES/HERMES (smm_svs_herc) sequence in XA twix format.
  • Changed behaviour of Siemens DICOM spec2nii dicom to recursively glob directory argument.
  • Better error output when encountering MR Image SOPClassUID.

0.6.1 (Wednesday 18th January 2023)

  • Fixed conjugation issue introduced by new nifti-mrs package dependency
  • SPAR/SDAT pipeline now handles HYPER special case.
  • Data/list pipeline now handles HYPER special case.
  • Fixed issue with XA Twix PatientSex and TxOffset attributes.
  • Re-enable Bruker conversion.

0.6.0 (Wednesday 11th January 2023)

  • NIfTI-MRS creation/handling/verification now performed by nifti-mrs package.

0.5.0 (Friday 2nd December 2022)

  • NIfTI-MRS version 0.6
  • Handle locale specific decimal separators in rda format.
  • Added special-case handling of the mgs_svs_ed(_universal) for twix data inputs.
  • Modified repository structure. Siemens and Philips files now have dedicated directories.
  • Support Python 3.11
  • Enable automatic Pypi upload and move to pyproject.toml file build.
  • Bruker conversion currently limited to numpy installations <1.20.0. Awaiting brukerapi package update.

0.4.9 (Friday 4th November 2022)

  • Handle FID sequence in twix converter.
  • Code lint updates
  • Updated versioneer.

0.4.8 (Sunday 2nd October 2022)

  • Updated citation information with publication of NIfTI-MRS paper.
  • Updated README information.
  • Added check that file had been written successfully.
  • Minor under the hood changes

0.4.7 (Sunday 11th September 2022)

  • Add tests for previous Siemens SOP UID DICOM types from VB line scanners.
  • Fixed bug in Siemens RDA header read. Still no orientation tests for RDA format.
  • Siemens VX line dicom files will now sum arrays of TE values.
  • Added better ID of the Siemens implementation of the standardised SLASER sequence (as DICOM).
  • Added provisional support for the GE slaser_cni sequence.
  • Added handling of LCModel RAW files lacking header information.
  • Included code and spelling fixes kindly contributed by Dimitri Papadopoulos

0.4.6 (Friday 8th July 2022)

  • Fix GE p file incorrect TR and TE. Were expressed in microseconds.

0.4.5 (Friday 8th July 2022)

  • Improved handling of Siemens DICOM files. Now explicitly handle Siemens Syngo Non Image Storage or MRSpectroscopyStorage DICOM types, regardless of scanner baseline.

0.4.4 (Thursday 28th April 2022)

  • Improved handling of Philips enhanced DICOM
  • WIP handling of Philips classic DICOM, more test data required.
  • SPAR/SDAT Philips data can now be reshaped ont eh command line using the -s and -t commands.
  • Corrected phase convention for Siemens NumarisX (XA) line DICOM data. This was reversed (conjugated) compared to VX line.