.IM (MIDAS) file format load:  performed corrections
a) SwapOrder, SignedShort flags were uninitialized  when the format is different from ANALYZE.
b) File size defect in the VA_RAW_FileUINT16interval function

BiCal paper:  Finished positioning of the landmarks on the Brain7T dataset (17 volumes),  Breast Phantom (24 volumes).

Rat Brain registration:  resolved the quality problem by adding and additional (5th) landmark at the back of the brain in the Eyes Plain.  Apparently the 4 Landmark configuration was too close to a Coplanar that was causing the Affine registration to fail.

Additional BrainBack landmark

Affine registration result:  Transformed CT overlaid by the MR-template landmarks.

CT layer (Green) overlaid with transparency on top of the MR layer (Red)

BiCal Smooth preprocess:   Changed the algorithm and the User Interface item to a simple checkbox (ON\OFF).  This finally makes BiCal with all parameter Quasi-constants.  I.e. User can run the BiCal on all volumes with very good result without changing parameter.  The eliminated SmoothPower parameter was extremely challenging to replace.

FireVoxel Build 225 is released.

Layer Operations: fixed 3 defect in BitOperations and ArithmeticOperations.

BiCal parameter Dialog: Changed the principal parameter from the field degree to FieldPrecision (mm). This would make the UI easier, f.e. User would not have to adjust the parameters after cropping the volume.

Verified the correct 4-landmark registration between MR-Template and the CT-volume.
The landmarks on eyes match very well.

Landmark positioning crash defect:  corrected the window rectangle invalidation legacy code.

Performed code re-engineering and simplification in preparation for the Methods section write up.

Edge-Constrained volume smooth (sometimes called ObjectSmooth or QuasiSegmentation in FireVoxel):  implemented a Zero-Edge variant when the thickness of the edges is 0 instead of current 1-voxel.  This allows not to use artificially higher resolution for better result.

Smoothed power=80

This is one of the principal components of the BiCal. But also it has a big potential to improve other operations, possibly MagTrace, and as as the pre-processing for more complex segmentations.

BiCal functionality:
"Low signal level" parameter has replaced the "Air Threshold" parameter.  The new parameter is quasi-constant ( in [5,10] range) and is independent of the volume content.

Separated the notion of  Air Threshold and the Signal-to-Gradient ration.  They produce separate masks now.  Air-Threshold can be defined very approximately now and completely automatically without User Input, as it is mostly used cosmetically to make the resulting volume to look without Air amplification.  Another component, the areas of the low Signal-to-Gradient ratio are excluded and this improves the Non-Uniformity measures substantially.


For the reference image, BPD-7T, with the same parameters the measures for
Build 223: WM\GM\CSM improved from   Build 224: 0.14\0.16\0.045  down to   0.07\0.14\0.031

ORIGINAL

After BICAL

FireVoxel Build 223 is released.

Dynamic Experiment\"ROI as a single TAC" mode:  removed the redundant residual\RMSE combination.

Non-Uniformity measurement reporting:  ensured that the Dark/Bright ratio is always displayed independent from layer order.

Removed the menu item:  "Measure Non-uniformity with paired seeds", since more advanced and easier function is available now.

Performed optimization of BiCal algorithm and code. Almost 100% parallelization is achieved.

On the reference Brain-7T volumes execution time was reduced from 202 sec down to 49 sec.

BiCal profiling result (see diagram below):

1.  Starts with Edge detection - virtually 100% parallel.
2.  Then processing start and separate peaks corresponds to iterations
with the increasing degree of Legendre polynomials.
3.  As degree grows, the SVD (= fully parallel) portion grows so the total
core load grows too.

I will be addressing the non-parallelized part discovered with VC++ Profiler.

FireVoxel Build 222 is released.

Support the "Scale Factor" field in the MIDAS file format.