v1.0.0

The major first release v1.0.0 of hMRI-toolbox.

[v1.0.0]

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
save LCPCA-denoising supplementary files as nifti instead of .mat
parameter error maps
robust combination of two runs using error maps
add .orig file extension to .gitignore to prevent merge artifacts to be pushed
update GUI code to enhance documentation for Proc. Smoothing
denoising module (lcpca): set mat_intent fields to input file values instead of spm_create_vol setting of 'aligned'
denoising module-second part: MPPCA denoising
added imperfect spoiling correction coefficients for common FIL protocols (3T and 7T).
Note that these coefficients are computed without the small angle approximation.
Update defaults with new recommended options: no more small angle approximation, and using weighted least squares R2* fitting

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
more informative error if optimization toolbox not present during NLLS R2* calculation
fix 3D-EPI B1 mapping not using b1defaults for Triotim scanner
use cell- instead of char- array to accommodate filenames of unequal length in RFsens
prevent missing B1 map for MTsat spamming the log
fix when no TE provided in 3DEPI SE/STE B1 mapping data
fixes compatibility with spm/spm required due to refactoring that removed TEMPLATE field
do not log ISC-applied to R1 in case of no-B1-corr and UNICORT
account for diffusion while gradients are off when calculating imperfect spoiling correction parameters
apply shift and diffusion operators in the correct order when calculating imperfect spoiling correction parameters
Default AFI TR2/TR1 value now matches typical sequence order

Old, unused imperfect spoiling correction coefficients have been removed and replaced with new ones.
If you need the old coefficients, you will need to add them back using a local defaults file.
Fix inconsistency between new implementation of PD and old T2* weighting removal method
Update imperfect spoiling correction with upstream bugfixes in EPG-X so computed coefficients will be different
Default AFI TR2/TR1 value now based on the second input image having the longer TR, which may not be the case for older data