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.

Fixed Object selection defect:  Staring from empty selection in certain situations a VROI was clicked to select but the "Selection Tracker" failed to show up leaving the User confused.

CT-real (rat) dataset - fixed the defect when it was not possible to place a 2nd landmark anywhere.

IM file format:  fixed the legacy file load with 8-bit voxels and non-trivial   "minimal value"\"maximum value" fields.

Major improvements to BiCal using new SVD-Parallel Jacobi:
a)  Was able to process much higher degrees of the polynomial - 25 from previous max 15.  New
image looks great and better.  Not able to do it in previous versions due to numerical instability of the
20000x20000 matrix solution using old SVD-NumericalRecipes (QR-decomposition).  Jacobi algorithm is simpler but more stable.
b)  At Degree=10 SVD takes 1% of calculation time, at 25 degree it takes 99% of calculation  time.
But now SVD is 100% parallel and scalable with 10x faster than  previous version.
c) On BPD datasets,  results for      WM/GM/CSM improved from  0.14/0.14/0.064  down to 0.10/0.11/0.49 for degree 25.
d) But calculation times become prohibitive at the higher degress ~40 min.

Completely re-engineered the CPU Capabilities Info function.  Newest processor and more reliable processing is available now.

Incorporated, debugged and improved the code for SVD: Jacobi One-sided block method.
Speed increase of about x5 times on  1000x1000 matrix comparing to serial version.

Nun-Uniformity Menu:  the Class Separation Measure function now displays the Optimal Threshold too.

Fully implemented  PET-CT-Atlas\Rodent workflow. Tested on the Rat dataset with 30-region Atlas.

New Layer Control dialog:  implemented
a) Enable All, Disable All buttons
b) ROI operations "Combine" button with a dialog option to remove the Source Operands layers.

Build 219 is released.

New Layer Control dialog:   Enabled "Open DICOM" and "Open RAW" items.

New Layer Control dialog:  enabled the "New ROI 3D" and "New ROI 4D" buttons.

New Layer Control dialog:  Enabled the ViewFilter button and functionality.

New Layer Control dialog:  added Left Doubleclick processing (name change edit\Ctrl ROI midslice jump)

New Layer control dialog: Added the "Info" button handler.

"Hover over ROI atlas" functionality was added. When there is an Atlas-like combination of ROIs is present, mouse cursor position is analyzed and the name of the single ROI layer is displayed that present at the mouse coordinate.

ROI compression\RAM allocation:  fixed major inefficiency defect, so that the RAM requirement for the 174 ROI atlas was reduced from 1GB down to 20 MB.

Old Layer Control dialog:  fixed the crash when  number of layers was exceeding the maximum (21).

Expanded the Atlas->ROI conversion function.  Tested on 174 ROI atlas.
Some performance issues have to be addressed with such high number of ROIs.

New Layer control dialog Added "Up\Down layer"

Enabled the Transparency-Slider functionality inside the new Layer Control Dialog box.

New Layer Control dialog box:

Added the "Active voxel layer" info dialog box and the GoTo (to Advance and Select Active layer) function.

Cursor hovering over the active layer with Real values now displays  "Real= ...value"

Implemented the ABT subtests for the DDC\Alpha model, new IVIM, IVIM-segmented models with the new parameters.

Implemented the ABT subtests for the DDC\Alpha model, new IVIM, IVIM-segmented models with the new parameters.

Added new Dynamic Model:  "DDC Stretched Exponential fit S = S0*(exp(-b*ADC)^alpha)"

Tested on the standard ABT dataset identical to ADC:

DDC fit:  DDC=0.0016, alpha=0.34, Residual=2.03

For comparison, we performed the ADC fit on the same data:

ADC fit:  ADC=0.001152, Residual=12

Corresponding Alpha-map processed over the ROI

IVIM (Basic and Segmented) models:  changed the output parameter  Dt ->  Dt*(1-f)

Re-engineered core Global Optimization Engine.

FireVoxel 217C is released.

"IVIM Segmented" model:  fixed defect when incorrect  Dp*f and Dt*f were output.

Build 217B is released.

1. Renamed the "MainMenu>VROI" ->  "MainMenu>Vector".
2.  Duplicated the "Rasterize Vector Entity" button of the main toolbar
under the "Main Menu>Vector>Rasterize".
3. Removed Rasterize items from "MainMenu>Trace"

IVIM {Basic,Segmented} models:  implemented new parameters "Dp*f" and "Dt*f" available to the user.

RAW   *.time file format:  implemented a support of variable naming convention when the index of the separate timepoint could contain arbitrary number of leading zeroes.

Build 217A is released.

Implemented corrections due to new features of Slope\Intercept fields present in RAW images.

Build 217 is released.

ANALYZE with the negative value:  implemented the dialog box that show the loading options when the negative values are detected in the ANALYZE file.  This replaces several separate dialog boxes used in earlier versions.

SPM-generated ANALYZE 4D volume containing variable (Slope,Intercept) values for different timepoints:  enabled the correct load consistent with the Mango package.

Fixed the Huffman compression to allow loading the volume with the 2000x2400 slice.

Finalized N4-Explorer including the Dialog box

N4Explorer: preparatory work with APIs so the optimizations structures and code of the BiCalExplorer could be fitted without any change.

BiCal run on 4 volumes:

80 positions per volume were estimated. Total execution is 7+ hours.  We varied the smoothing power [0,100] and the polynomial degree [6,13].

"Class separation measure":  was reduced from the original  0.173 down to 0.003

Resulting optimal BiCal parameters are:

BiCal explorer:  completely implemented including the specialized Dialog box.
This optimization works for a single volume at the moment.

FireVoxel Build 216B is released.

N4-UI function:  since the output is real, added the REAL->INT postprocessing conversion to match the Source volume type.

Implemented the "Misclassification of the Optimial Separation" function and the User Interface under "MainMenu>Nonuniformity". Function is fully parallel and executes very fast.

"MainMenu>Measurement>Hausdorff Distance":
Implemented the Hausdorff distance measure {Edge,Area} variants.

Build 216 is released.

• RasterPaintbrush  Tool\Dialog:  fixed the defect when the SmartZoom option setting was not remembered.
• N4-tool:  implemented the option Output field.
• N4 dialog box:  replace the "Field Smoothness" name with the "Spline Distance" to emphasize difference with the NYU-N3 tool between those 2 terms.
• N3-NYU tool:  fixed the crash for large values of the "Field Smoothness" = 200.
• N4 crash defect, with supplied parameters (iter=75): fixed.
• Non-Uniformity Measurement:  fixed a defect that exactly two ROI layers are required for the measurement.
• Now any number of ROIs might be present, as long as only two are ENABLED.
• Non-Uniformity measurement:  implemented function and Menu Item to measure 2 sets of blobs that are not completely paired.  This allows to measure non-uniformity more completely, while using the paired blobs for constraints.

RasterPaintbrush  Tool\Dialog:  fixed the defect when the SmartZoom option setting was not remembered.

N4-tool:  implemented the option Output field.

N4 dialog box:  replace the "Field Smoothness" name with the "Spline Distance" to emphasize difference with the NYU-N3 tool between those 2 terms.

N3-NYU tool:  fixed the crash for large values of the "Field Smoothness" = 200.

N4 crash defect, with supplied parameters (iter=75): fixed.

Non-Uniformity Measurement:  fixed a defect that exactly two ROI layers are required for the measurement.
Now any number of ROIs might be present, as long as only two are ENABLED.

Non-Uniformity measurement:  implemented function and Menu Item to measure 2 sets of blobs that are not completely paired.  This allows to measure non-uniformity more completely, while using the paired blobs for constraints.

FireVoxel Build 215 is released.

Non-uniformity\Two tissue Contrast measurement:  improved diagnostics when there is no full blob pairing between the tissues.

Finished the integration of the N4 bias correction binary tool.  This includes the new N4 dialog box:

NIFTI-1 file format (.NII):  implemented Save (UI) for the integer volumes.

FireVoxel Build 214A is released.

MagPoly dialog box: eliminated defect due to the dangling variable m_SnapToCurve. This was only partially eliminated before and was getting some random values.

Added the  "Integer Volume - to - Real Volume" conversion function.  Moved  both conversion functions under the same submenu  under  MainMenu>Volume

FireVoxel Build 214 is released.

MagTrace, Raster Paintbrush SmartZoom:  If the image is fully visible on the current zoom, there will be no action by the SmartZoom adjusting the document window.

Raster Paintbrush:  implemented SmartZoom for automatically shifting Zoom Window.

Enabled Ctrl+\Ctrl- zooming while inside  the MagTrace tool.

MagTrace: Implemented "Smart Zoom" feature.  When the User moves and clicks the Snap cursor, the viewing window position shifts so that its center matches the position of the cursor.

Enabled Acceletators
Ctrl+   :   Zoom In
Ctrl-   :    Zoom Out

Added the "Forward only" option for MagTrace so the new snapping position is only forward with the respect to the vector between the previous fixed point and the current user specified position.

Enabled the ViewFilter on the Parametric map image type volume.

Polyline\Spline control point hand shape: changed to semitransparent circle:

FireVoxel  Build 212 is released.

Implemented the FVX-file format Load\Save  incorporating the Splines\Polylines.

Polygon control points: change the style to the semitransparent filled rectangle.

This also solves the problem when the contour is copied,
resnapped. In previous version two points were snapped to the same coordinates, so the control point were becoming invisible.

Spline\Polyline entities: fixed the defect when the control point is selected, moved outside the document area and becomes unreachable.

Added the menu item   MainMenu>Trace>MagTrace

Implemented a support function to output the Edges used by MagTrace for the current slice.
Currently selected MagTrace parameters are used so it is a 1-click operation.

Corrected the "HitTest" on mouse click over the Spline entity.

Corrected the defect for the HitTest mouse click on the polyline.

Modified the ToolTip for the "Width\Level" button of the Main toolbar.

Added   "MainMenu>Trace>Application specific settings" ability for {Femur,Hippocampus} applications.