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hMRI-toolbox changelog

This changelog documents all notable changes to the hMRI-toolbox.

Most recent version numbers should follow the Semantic Versioning principles (e.g. bug fixes: x.x.1 > x.x.2, new feature with backward compatibility: x.2.x > x.3.0, major release affecting the way data are handled and processed: 1.x.x > 2.0.0).

[unreleased]

Added

  • option to choose different models and parameters for B1-correction of MTsat
  • set default WM percent value in hmri_defaults.
  • spatial processing: add explicit mask creation and fix implicit mask (0 to NaN in float images)
  • update FIL seste seq parameters in get_metadata_val_classic
  • denoising module-first part: Java-Matlab interface for LCPCA denoising
  • read EffectiveEchoTime in new TerraX Dicom format

Fixed

  • replace datestr(now) with datetime('now') in line with MATLAB recommendation
  • fix crash if input images have different matrix sizes, and warn
  • make B1-map creation using 3DEPI SE/STE and AFI methods fall back to defaults without sidecar files, rather than crash
  • Modify the filenames as files are copied to RFsensCalc to prevent overwriting in further processing
  • batch interface now enforces the number of B1 input images correctly for B1 mapping methods which only need two images.
  • fix error if optimization toolbox not present during NLLS R2* calculation

[v0.6.1]

Fixed

  • The local config files have been converted to scripts for compatibility with compiled version
  • function-evaluate SPM-struct (preproc8.val) for SPM development version compatibility.
  • copy acquisition metadata to TE=0 volumes in Results/Supplementary folder after map creation so they can be used as input to the toolbox if needed

[v0.6.0]

Added

  • support for reading RepetitionTime from individual file metadata for AFI B1-mapping data (i.e. support for qMRI-BIDS formatted data)

Fixed

  • issue #5: fixed version check for compiled toolbox
  • QUIQI check: dependence on stats toolbox
  • issue #14 (Spatial processing: Inverse deformation field moved along with forward deformation field to requested folder)
  • issue #59: both the qform and the sform of the first PD-weighted image are now propagated to the quantitative maps, rather than just the sform
  • Add OSF interface to download test files directly from the online storage

Breaking changes

  • AFI B1 mapping data must be entered in the opposite order to previously (for sequence programmers: the assumption is now made that the order of alTR strictly reflects the order of acquisition, rather than being sorted). A warning will be printed if the toolbox detects that the data might have been provided in the wrong order (see changes made in #41). Note that while this is a breaking change, it should make data sorting more logical.

[v0.5.0]

Added

  • double angle mapping (DAM) B1 mapping option
  • option to test ambiguous angle ranges beyond [0,90] and [90,180] degrees for SE/STE B1 mapping (nAmbiguousAngles b1 defaults parameter)
  • various B1 input checking
  • smoothing and masking options for all appropriate B1 mapping methods

Fixed

  • issue #42 (Non-matching filename length can cause AFI B1 calculation crash)
  • issue #46 (Toolbox expects SE/STE input sorted by echo and flip angle whereas BIDS sorts by flip angle then echo)
  • issue #26 (Possible bug in calculation of B1 maps with SE/STE EPI)
  • SE/STE B1 mapping calculation can now no longer select both ambiguous angles for a given SE/STE pair

[v0.4.0]

Added

  • weighted least squares R2* fitting
  • cleaner input/output functions for map creation
  • several unit tests
  • nulling of bright voxels during unified segmentation to improve segmentation of anonymised data

[v0.3.0]

Added

  • QUIQI
  • quality control tool

[v0.2.6]

Fixed

  • Make cell processing code run for all paths of get_metadata_val so that TR, TE and FA can be read from the nifti description field if needed

[v0.2.5]

  • Provides option to remove the small angle approximation when calculating R1 and PD
  • Bugfix for reverse phase encoding direction 3D-EPI on Siemens scanners
  • Experimental BIDS support

[v0.2.4]

  • added back accidentally removed B1 mapping options

[v0.2.3]

  • allow calculation of B1 maps independently of the rest of the quantitative maps

[v0.2.2]

  • fix problem with broken JSON serialisation
  • open files read only where possible

[v0.2.1]

fix for issue #6

[v0.2.0]

Fixed

Many small bugs - refer to commits for details...

Added

  • DICOM import for Philips data:
    Properly accounts for the rescaling factor for quantitative analysis (see Chenevert et al. 2014).

  • Tracking Matlab version number in the JSON metadata.

Changed

  • MT saturation map file name from *_MT to *_MTsat.

[v0.1.2-beta]

Fixed

Many small bugs - refer to commits for details...

Added

  • Single echo VFA approach: Implemented with a default minimum number of echoes for R2* calculation of 4. The number of echoes used is logged and a general warning informs the user about data interpretation when R2* map derived from only a few echoes.

  • Metadata & processing parameters: Bunch of modifications to improve the readability and completeness of the metadata, for each output image as well as for the processing parameters.

  • UNICORT-generated R1 and B1 to calculate PD and MT maps: This option has not been thoroughly tested. Made available under "ADVANCED USERS ONLY": the option to use the R1-UNICORT-derived B1 map for B1 transmit bias correction in PD and MT maps can only be enabled by an advanced user implementing customized defaults.

  • Example files: For defaults customization and toolbox configuration examples.

  • New option to disable the coregistration steps: Coregistration shouldn't be disabled but it can be convenient in specific cases (simulated data, phantom data). Option made available under "ADVANCED USERS ONLY", i.e. can only be modified by an advanced user implementing customized defaults. When enabled (defaults), all input images to hmri_create_MTProt.m (transmit and receive fields, T1w and MTw images) are coregistered to the PDw average (or TE=0 fit) image (see hmri_create_MTProt.m).

Changed

  • Options for RF sensitivity bias field correction: The available options are now None, Unified Segmentation(default), Single and Per contrast. Beware that the previously implemented Noneoption corresponds to the current Unified Segmentation!!! Batch files saved with the previous version are not fully compatible with the current version and must be adapted.

[v0.1.1-beta]

First public beta-version of the hMRI-toolbox.

Modular structure including the following modules:

  • Configure toolbox
  • DICOM Import
  • Auto-Reorient
  • Create hMRI maps
  • Process hMRI maps

[v0.2.0] (released 2018-12-20)

Fixed

Many small bugs - refer to commits for details...

Added

  • DICOM import for Philips data:
    Properly accounts for the rescaling factor for quantitative analysis (see Chenevert et al. 2014).

  • Tracking Matlab version number in the JSON metadata.

Changed

  • MT saturation map file name from *_MT to *_MTsat.

[v0.1.2-beta2] (released 2018-07-30)

Fixed

Many small bugs - refer to commits for details...

Added

  • Rescaling factor to pre-processed B1: To deal with B1 maps that are not in p.u. of the nominal flip angle. Percent units expected by the hMRI-toolbox, but... The current BIDS proposal is to have B1 maps scaled so that a value of 1 corresponds to the nominal flip angle. To be continued...

  • Logging processing messages: In order to review and keep track of info, warnings and other messages coming up during data processing, all messages are logged using the hmri_log.m script. Various options available (pop-up messages, messages logged to the Matlab Command Window, messages saved into a log file). Improved tracking and readability of the messages, with more explicit descriptions and improved uniformity of the used format.

Changed

  • Imperfect spoiling correction disabled by default: To avoid confusion and resulting mistake (applying correction coefficients to the wrong sequence). With the publication of "standard MPM protocols", it is likely to have new protocols implemented with sequences other than the customised sequences for which the correction coefficients have been calculated. Therefore the TR and FA criteria are not sufficient any longer to identify the right set of correction coeficients to be used unambiguously :/...

[v0.1.2-beta] (released 2018-06-15)

Fixed

Many small bugs - refer to commits for details...

Added

  • Single echo VFA approach: Implemented with a default minimum number of echoes for R2* calculation of 4. The number of echoes used is logged and a general warning informs the user about data interpretation when R2* map derived from only a few echoes.

  • Metadata & processing parameters: Bunch of modifications to improve the readability and completeness of the metadata, for each output image as well as for the processing parameters.

  • UNICORT-generated R1 and B1 to calculate PD and MT maps: This option has not been thoroughly tested. Made available under "ADVANCED USERS ONLY": the option to use the R1-UNICORT-derived B1 map for B1 transmit bias correction in PD and MT maps can only be enabled by an advanced user implementing customized defaults.

  • Example files: For defaults customization and toolbox configuration examples.

  • New option to disable the coregistration steps: Coregistration shouldn't be disabled but it can be convenient in specific cases (simulated data, phantom data). Option made available under "ADVANCED USERS ONLY", i.e. can only be modified by an advanced user implementing customized defaults. When enabled (defaults), all input images to hmri_create_MTProt.m (transmit and receive fields, T1w and MTw images) are coregistered to the PDw average (or TE=0 fit) image (see hmri_create_MTProt.m).

Changed

  • Options for RF sensitivity bias field correction: The available options are now None, Unified Segmentation(default), Single and Per contrast. Beware that the previously implemented Noneoption corresponded to the current Unified Segmentation!!! Batch files saved with the previous version are not fully compatible with the current version and must be adapted.

[v0.1.1-beta] (released 2017-11-14)

First public beta-version of the hMRI-toolbox.

Modular structure including the following modules:

  • Configure toolbox
  • DICOM Import
  • Auto-Reorient
  • Create hMRI maps
  • Process hMRI maps

[v0.1.0] (released 2016-11-02)

First stable version of the VBQ toolbox

Considered as mainstream among the various sites taking part in the project and starting point for the hMRI-toolbox development.