v0.6.1

[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

[standalone-hMRItoolboxv0.6.1.zip]

Compiled with:

-Matlab version: 9.14.0.2239454 (R2023a) Update 1
-OS version: Debian GNU/Linux 11 (bullseye)

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

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

• QUIQI added
• visual quality control tool added

v0.2.6

fixes:

• Backwards compatibility restored: TR, TE and FA can now again 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

Allows calculation of B1 maps independently of the rest of the quantitative maps

bugfix release v0.2.2

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