N3-nonuniformity correction tool - enabled to work with Real-valued volumes.

Enabled BiCal to work with the Real-value images. Processed sodium image with BiCal.

Original Sodium image

BiCal processed sodium image

Fixed the "total non-function" defect in VA_VolMul (Volume Multiply) function. This was used in Sulci Depth detection and BiCal.

Implemented initial version of perivascular space segmentation under
"MainMenu>Segment>Detect Bright Spots".

Implemented the dialog for the perivascular space segmentation.

DICOM open dialog:   fixed the loading problem when very long path of the DICOM file is specified.

Fixed crash defect: in Dialog Open DICOM:  when Browse functionality is used to change the DICOM folder, pressing the Info button causes the crash.

Fixed entropy calculation

FireVoxel Build 199 is released.

1.Added submenu   MainMenu>Applications>Breast MR FTG>Correct non-uniformity using BiCal. Provided initial parameter set for non-uniformity correction.
2.  ROI>Convert ROI to VROI:  after the operation is completed, zooming to the center of the last VROI.
3. Replaced the corresponding menu item:  "Enclose connected components by Vector ROIs". MainMenu>Volume>Crop with 4D Vector ROI. Fixed the messages in case of unsuitable objects and\or selections.
4. Added "implicit selection", i.e. if a single non-selected VROI is present, it will be treated as the selection.
5.Majority of the FireVoxel dialog boxes (33 total):  Merged the header and source file of the dialog.  Reduced each occurrence of the Dialog call down to a single line, f.e.   "FV_DlgBical( Parm)
6. Code engineering:  moved the CVol class from the FireVoxel project (mostly user interface) to the VolumeAnalyze project (mostly algorithms).
7. Dialog RoiStats3D:  integrated histogram splitting into N segments so that the in-class variance is minimized.
8. Menu item   "MainMenu>ROI>Layer Operations" is moved to "MainMenu>Volume>Layer Operations".
9.  Dialog RoiStats3D: Fixed calculation of the Skewness and Kurtosis. Added the information about entropy for the current binning of the histogram. Change the format of the ROI information.
10. Dynamic Processing module:  fixed a bug when variable was not initialized in case the voxel was not processed and the VOIDVOX values had to be output.
11.On Mouse move handling:  in the recent Builds we added the requirement of holding the Shift key to enable operation of tools such as {VectorROI,ZoomByWindow} etc.  This was due to the addition of the Window Center\Width functionality that required to analyze regular moves. Now this requirement of pressing Shift is removed (i.e. UI restored to the pre-Build 196 state).
12. Auto Build Test:  added the subtest for ADC maps.
13. Dynamic Experiment Extrapolation framework:  added User Interface to specify additional dynamic coordinates to ones already present in the experiment. Fully implemented Extrapolation with all features for {ADC,Kurtosis,Sokoloff} models. Dynamic Experiment dialog:  implemented the "Extrapolate" button and corresponding programming support for all models (only    {Kurtosis,Sokoloff} are supported).
14. Perform code maintenance and optimizations in DynExp.cpp responsible for the mid-layer of the Dynamic Processing models.

Added submenu   MainMenu>Applications>Breast MR FTG>Correct non-uniformity using BiCal.
Provided initial parameter set for non-uniformity correction.

BiCal vs. N3   NU-correction result comparison

BiCal   3-14-60

N3-default

1.  ROI>Convert ROI to VROI:  after the operation is completed, the view centers on the center of the last VROI completed.

2. Replaced the corresponding menu item:  "Enclose connected components by Vector ROIs"

MainMenu>Volume>Crop with 4D Vector ROI
1.  Fixed the messages in case of unsuitable objects and\or selections.
2.  Added "implicit selection", i.e. if a single non-selected VROI is present, it will be treated as the selection.

Majority of the FireVoxel dialog boxes (33 total):  Merged the header and source file of the dialog.  Reduced each occurrence of the Dialog call down to a single line, f.e.   "FV_DlgBical( Parm)

Histogram split by "minimize in-class variance" in sample1.fvx

Code engineering:  moved the CVol class from the FireVoxel project (mostly user interface) to the VolumeAnalyze project (mostly algorithms).

Quick test of the "Perivascular space segmentation algorithm"

Dense breast processing example - segment out fat  using "Segment Bright Ridges"

"Segment ducts" algorithm using the "Segment dark ridges" function.

Breast image:   N3 vs. BiCal comparison.

N3                                                                      BiCal

Dialog RoiStats3D:  integrated histogram splitting into N segments so that the in-class variance is minimized.  

Menu item   "MainMenu>ROI>Layer Operations" is moved to "MainMenu>Volume>Layer Operations".

Dialog RoiStats3D: Fixed calculation of the Skewness and Kurtosis.

Example of the chest wall separation using the "Fill & Morph Arc" function.  Original contours in Blue are drawn 10 slices apart.  Red contours are generated by Morph function.

Dialog Roi Stats3D:   added the information about entropy for the current binning of the histogram

Change the format of the ROI information.

Dynamic Processing module:  fixed a bug when variable was not initialized in case the voxel was not processed and the VOIDVOX values had to be output.

On Mouse move handling:  in the recent Builds we added the requirement of holding the Shift key to enable operation of tools such as {VectorROI,ZoomByWindow} etc.  This was due to the addition of the Window Center\Width functionality that required to analyze regular moves.

Now this requirement of pressing Shift is removed (i.e. UI restored to the pre-Build 196 state).
The only tool that requires pressing Shift is "Select by Window".

Window center\width is working as advertised.

Auto Build Test:  added the subtest for ADC maps.

Dynamic Experiment Extrapolation framework:  added User Interface to specify additional dynamic coordinates to ones already present in the experiment.
Fully implemented Extrapolation with all features for {ADC,Kurtosis,Sokoloff} models.

Dynamic Experiment dialog:  implemented the "Extrapolate" button and corresponding programming support for all models (only    {Kurtosis,Sokoloff} are supported).
This framework would allow to construct synthetic "Extrapolated" volumes that would contain only modeled voxels for some or all dynamic coordinates.

Perform code maintenance and optimizations in DynExp.cpp responsible for the mid-layer of the Dynamic Processing models.

FireVoxel Build 198 is released.

1. Dialog RoiStats3D: Added a functionality to control Number of Bins in the Histogram.  User enters the number and to update the histogram the focus should leave the field (press Tab).
2. "Mouse windowing" of the SI->display mapping:  changed the orientation of the vertical movement when the up vertical movement increases the value of the Window center.
3. RoiStats3D dialog:  added   Histogram Skewness and Kurtosis to information panel.
4. Spacebar button would maximize the Document View.

Document View window:  Maximize when the spacebar button is pressed.

Dialog RoiStats3D: Added a functionality to control Number of Bins in the Histogram.  User enters the number and to update the histogram the focus should leave the field (press Tab).

"Mouse windowing" of the SI->display mapping:  changed the orientation of the vertical movement when the up vertical movement increases the value of the Window center.

RoiStats3D dialog:  added   Histogram Skewness and Kurtosis to information panel.

FireVoxel Build 197 is released:

1. FireVoxel\DLLs\DCMTK - moved the whole code base entirely into "8-byte structure tag alignment" to avoid any sideeffects of different module alignment.
2. Added a functionality to change Signal  Window Center\Width settings using mouse movement with the Left Mouse button pressed.
3. Fixed the crash on  ROI image only (without SI volume) when the RoiStats3D dialog (F3) is activated.
4. Color Dialog defects:  fixed the   "always 0 color" and "crash on the exit" defects by recompiling the FireVoxel.exe module with 8-byte alignment.
5. Replaced all numerical ("double float") fields handling within all of the 76 Dialog boxes in FireVoxel.
6. MFC dialog "double float" numerical field failure:  developed a workaround by replacing MFC function:   AFXAPI DDX_Text(CDataExchange* pDX, int nIDC, double& value)
7. Completely removed the Intel\TBB library from FireVoxel.exe and all DLLs.  This was replaced with the Microsoft's native library <ppl.h>.  Dependency on the VC++ 2013 redistributable was removed from the FireVoxel.
8. All higher level DICOM processing function (incl.  Constructing DICOM tree, etc) - was moved out of the main FireVoxel.exe to the VolumeAnalyze. dll.  This is to improve the architecture by leaving only the User-Interface functionality in .exe while moving all the math and processing into the dll.
9. Fixed the defect when after running the "Segment Whole Kidney with blanket", the Volume display interpolation would always reset to FALSE.
10. Implemented new model:  Sokoloff (Short formula) with 2 Input functions and Double Pass (with optional parameter fixing after the first pass).

FireVoxel\DLLs\DCMTK - moved the whole code base entirely into "8-byte structure tag alignment" to avoid any sideeffects of different module alignment.

Added a functionality to change Signal  Window Center\Width settings using mouse movement with the Left Mouse button pressed.
Vertical movement - changes Window Center
Horizontal movement - changes Window Width

Fixed the crash on  ROI image only (without SI volume) when the RoiStats3D dialog (F3) is activated.

Color Dialog defects:  fixed the   "always 0 color" and "crash on the exit" defects by recompiling the FireVoxel.exe module with 8-byte alignment.

Replaced all numerical ("double float") fields handling within all of the 76 Dialog boxes in FireVoxel.

MFC dialog "double float" numerical field failure:  developed a workaround by replacing MFC function:  

           AFXAPI DDX_Text(CDataExchange* pDX, int nIDC, double& value)

with the custom function.  This custom function will be in place till the MFC dialog problem is fixed.

Completely removed the Intel\TBB library from FireVoxel.exe and all DLLs.  This was replaced with the Microsoft's native library <ppl.h>.  Dependency on the VC++ 2013 redistributable was removed from the FireVoxel.

All higher level DICOM processing function (incl.  Constructing DICOM tree, etc) - was moved out of the main FireVoxel.exe to the VolumeAnalyze. dll.  This is to improve the architecture by leaving only the User-Interface functionality in .exe while moving all the math and processing into the dll.
This architecture is also more suitable to working with the command line modules if this would be required.

Diagnosed a major MS VC++ defect regarding the numerical input fields in MFC dialog boxes.
Came up with the workaround for standalone applications - fixing FireVoxel would require linking the FireVoxel project (UI part) with the debug version of the MFC.

Windows native CColorDialog contain a defect in current release of VC++ 2015.
Encapsulated this dialog within a standard call to avoid crash.  Replace all 6 occurrences of this dialog within other dialogs.

Fixed the defect when after running the "Segment Whole Kidney with blanket", the Volume display interpolation would always reset to FALSE.

Implemented new model:  Sokoloff (Short formula) with 2 Input functions and Double Pass (with optional parameter fixing after the first pass).

FireVoxel Build 196 is released.

1. Fully compiled and linked all the FireVoxel libraries in 64-bit mode.
2. Upgraded development environment to VC++ 2015 (v 14)
3. CFileDialog  (Load\Save) started to cause crash under VC++ 2015. This happened when the initial Directory path was specified during initialization.  Fixed the crash by setting the VistaStyle=0. It is purely Microsoft's bug so the flag is just a workaround.
4. DCMTK 64-bit reengineering: supplied an external definition for HostID and removed the DCMTK for obtaining network hostID that was crashing in 64-bit Release mode.
5. FireVoxel-64 bit is completely cleared on all ABT subtests in Debug|Release modes.
6. Fixed the b-value loading problem on the "*.time" 10-timepoint dataset from MSKCC.
7. Multi-projection crosshair cursor - corrected redrawing when the User paints with the paintbrush. Before the crosshair would only partially redraw leaving numerous lines on the screen.

Multi-projection crosshair cursor - corrected redrawing when the User paints with the paintbrush. Before the crosshair would only partially redraw leaving numerous lines on the screen.

Fixed the b-value loading problem on the "*.time" 10-timepoint dataset from MSKCC.

FireVoxel-64 bit is completely cleared on all ABT subtests in Debug|Release modes.

IN PROGRESS:   x64\Release - clearing up the ABT\Dynamic Processing subtest

DCMTK 64-bit reengineering: supplied an external definition for HostID and removed the DCMTK for obtaining network hostID that was crashing in 64-bit Release mode.

Cleared the FireVoxel- ABT-  Dynamic Experiment subtest with 64-bit application.

Verified the FireVoxel ABT-EdgeWave subtest for 64-bit application mode.

CFileDialog  (Load\Save) started to cause crash under VC++ 2015. This happened when the initial Directory path was specified during initialization.  Fixed the crash by setting the VistaStyle=0. It is purely Microsoft's bug so the flag is just a workaround.

FireVoxel64bit:  enabled loading of previous 32-bit FVX files and provided backward compatibility.

Upgraded development environment to VC++ 2015 (v 14)

Fully compiled and linked all the FireVoxel libraries in 64-bit mode.

DCMTK-OFFIS toolkit, produced the 64-bit version by eliminating makefile and constructing the VC++ project from the ground up.

FireVoxel Builds {193,194,195} are released.

1. Volume reslicing using polynomial transforms:  corrected imprecision defect due to incorrect rounding.
2. MainMenu>Volume>Smooth (and other smoothing operations):  restored correct operation on the ROI.
3. Sokoloff model (Short formula):  added additional user controls so the values of all parameters {K1,k2,k3} could be fixed during the optimization.  User simply set  k2_min = k2_max = Desired Value.
4. Sokoloff model (Long formula):  added additional user controls so the values of all parameters {K1,k2,k3} could be fixed during the optimization.  User simply set  k2_min = k2_max = Desired Value.
5. Enabled loading of the GE-scanner diffusion dataset by providing a specialized procedure to load    b-values from the private GE tags.
6. Corrected defect when FVX format file for storing the parameters of Dynamic Experiment are changed.
7. Implemented the "Blood Volume" User parameter for Sokoloff  Short\Long models.
8. Loading ANALYZE file:  fixed defect of incorrect truncation of signed negative numbers to 0.
9. Implemented new User- Interface-level function that produces all 6 projections of the SulciPrint3D directly from the BrainMask
10. Implemented User-level  Active volume "Mirror along axis" function. This is under "MainMenu>3D Projection>Mirror along axis".  Function is now working for all 3 axis {X,Y,Z}.
11. Corrected and updated the "Open TAC as 4D volume" function.  This allows user to specify the *.TXT file containing the TAC.
12. Implemented basic variant of Monte-carlo simulation for all Dynamic Models in FireVoxel.
13. Implemented a new menu "Dynamic Processing" in the MainFrame part of the processing (i.e. when no volume is required to be loading).
14. Implemented the functionality for F3\F4    Roi Stats  3D\4D:  when ROI is missing, function calculates stats for the ROI that covers the entire volume.
15. Dynamic Experiment framework: fixed defect in all models involving the Input Function(s).
16. Enabled that Concentration conversion parameters are remembered and then recalled between several calls to the corresponding dialog box.

In Menu items:
1. "MainFrame>Applications>Convert TAC to Concentration"
2. "Main Menu>4D Process>Convert TAC to Concentration"

Enabled that Concentration conversion parameters are remembered and then recalled between several calls to the corresponding dialog box.

Dynamic Experiment framework: fixed defect in all models involving the Input Function(s).
When Concentration conversion other than "Signal" was specified, the converted signal was posted
over the original signal data.  So on the following runs, the model calculations were entirely wrong.

Implemented the functionality for F3\F4    Roi Stats  3D\4D:  when ROI is missing, function calculates stats for the ROI that covers the entire volume.

Implemented a new menu "Dynamic Processing" in the MainFrame part of the processing (i.e. when no volume is required to be loading).

Implemented basic variant of Monte-carlo simulation for all Dynamic Models in FireVoxel.

User starts with obtaining the required ROI and saving it to the file.

User create a 4D-volume from the specified TAC setting the level of noise (10% in this example). Then runs the chosen model over the 4D volume, where each voxel corresponds to the original TAC+ random Noise.

Resulting is the map(s) of the selected parameters (K1 in this example).

Next user is able to do some basic statistics on the specified parameter, K1 in this case.

Corrected and updated the "Open TAC as 4D volume" function.  This allows user to specify the *.TXT file containing the TAC.  User specifies dimensions of the resulting volume where which voxel is constructed given the specified TAC + random Noise (Noise level is specified by the User).

This functionality allows to perform Monte-Carlo modelling of the Dynamic Models.

Single Timepoint of the resulting volume where vox(x,y,z) = TAC[t]+RandomNoise(x,y,z)

Implemented User-level  Active volume "Mirror along axis" function. This is under "MainMenu>3D Projection>Mirror along axis".  Function is now working for all 3 axis {X,Y,Z}.

Implemented new User- Interface-level function that produces all 6 projections of the SulciPrint3D directly from the BrainMask.  There is no need to generate intermediate   SulciPrint3D structure. Function is under the MainMenu>Applications>BrainPrint>Generate SulciPrint2D from BrainMask (6 projections).

Initial tests of the "Snowball" methodology for automatic fluid registrations, segmentations, and organ localization.  In one scenario we would try to locate both kidneys on the volume, fully automatically, using only sparsely defined library of shapes.

Red is a template shape approximating a kidney.  Current positioning describes a step of iterations when template is moving across the volume with some substantial step (but smaller than the Snowball capture radius).

After just few iterations of a fully automatic procedure, we end up with this localization.  It has a certain match score.  Hypothetically, an automatic localization algorithm might work simply traversing all possible positions with step (SX,SY,SZ)<Snowball Capture radius.  Position with the highest score is chosen.

This is just for illustration purposes, how primitive features are constructed at each step of the iteration.

Loading ANALYZE file:  fixed defect of incorrect truncation of signed negative numbers to 0.

Implemented the "Blood Volume" User parameter for Sokoloff  Short\Long models.

Saving Active Dynamic model settings to FVX file:  corrected a design flaw.  Sometimes we change the number of Free and Output parameters in the models.  If this model was save previously to FVX file as an Active model the current version of FireVoxel often would not be able to load such FireVoxel file and it will be lost.  In the corrected version, only the warning that the Model design was changed would show but file would always be loaded.

Enabled loading of the GE-scanner diffusion dataset by providing a specialized procedure to load                 b-values from the private GE tags.

Sokoloff model (Long formula):  added additional user controls so the values of all parameters {K1,k2,k3} could be fixed during the optimization.  User simply set  k2_min = k2_max = Desired Value.

Sokoloff model (Short formula):  added additional user controls so the values of all parameters {K1,k2,k3} could be fixed during the optimization.  User simply set  k2_min = k2_max = Desired Value.

MainMenu>Volume>Smooth (and other smoothing operations):  restored correct operation on the ROI.

Implemented a new variant of smoothing of the Sparse Vector Field obtained as a result of the feature match. Jacobian of the smooth field is within the specified interval at all the voxels of the volume.

Implemented a function to measure a jacobian of the transformation corresponding to the Vector Field.
Implemented an iterative smoothing function of the Vector Field till the jacobian at every voxel falls within the specified interval of values.

Experimenting with the Nearest-neighbor based estimation of the sparse vector Field (this is instead of traditional gaussian smoothing step used in the literature:  Demons,ART, etc)

Deformable registration/segmentation:  implemented and tested local affine transform functions around the "Focus of maximum displacement of the vector field"

Deformable registration:  experimented with using the Polynomial transforms obtained by Amoeba optimization using the Jacobian constraints.

Volume reslicing using polynomial transforms:  corrected imprecision defect due to incorrect rounding.

FireVoxel Build 192 is released.

1. Fixed the crash when  MainMenu>Register4D>AutoFocus 4D is called for the (2D+t) volumes.
2. LoadDicom dialog:  Composite series:
a) Fixed the crash when in dialog "Include composite Series"  NO is selected.
b) In case of the composite series, automatically popup the Range dialog box
to choose which subseries to load.
3. Open DICOM dialog:  fixed defect so that the complete path is remembered for the next opening of the dialog

Open DICOM dialog:  fixed defect so that the complete path is remembered for the next opening of the dialog.

LoadDicom dialog:  Composite series:
a) Fixed the crash when in dialog "Include composite Series"  NO is selected.
b) In case of the composite series, automatically popup the Range dialog box
to choose which subseries to load.

Fixed the crash when  MainMenu>Register4D>AutoFocus 4D is called for the (2D+t) volumes.

FireVoxel Build 191 is released.

1. MainMenu>3D Projection>{Make Isotropic,Rotate and Create New volume} functions.  Fixed defect when the function would run but resulting document would not be created.
2. 4D registration of a single slice Renal volume (CIR):  corrected defect that produced the message "Incorrect Isotropic resolution".
3. Single slice registration 3D\4D:   fixed defect when URAL\URALTAU measure would not work
4. AutoFocus registration (SingleSlice volumes):  corrected defect when constructing Target operand with Downscale>1.
5. CERENE3D workflow:  modified kidney registration menu to include separate items for 2D (CIR) and 3D (NUCS) datasets.

CERENE3D workflow:  modified kidney registration menu to include separate items for 2D (CIR) and 3D (NUCS) datasets.

Checking a potential problem in PERFUSION datasets.  There seem to be dark frames included at regular intervals in the dataset.  Is this OK?

Cleared the renal single slice registration dataset that was not registering well before, great registration quality.  Screenshot shows registration of Target ROI to one of the following timepoints (#8) that was not registered well before.

AutoFocus registration (SingleSlice volumes):  corrected defect when constructing Target operand with Downscale>1.

Single slice registration 3D\4D:   fixed defect when URAL\URALTAU measure would not work.  Defect was in improperly cleaning the margins of the gradient map in 2D case (whole map was set to 0).

4D registration of a single slice Renal volume (CIR):  corrected defect that produced the message "Incorrect Isotropic resolution".

MainMenu>3D Projection>{Make Isotropic,Rotate and Create New volume} functions.  Fixed defect when the function would run but resulting document would not be created.

FireVoxel Build 190 is released.

1. CERENE3D workflow Menu:  added "T1: Segment Kidney  {BLANKET,CONSTR}" items.
2. Breast lesion workflow:  corrected the defect in   PET->T1 registration when the SI volume has to be specifically Active resulting in the warning message
3. Dialog EdgeWaveLive: fixed the defect when changing one of the "Live parameters" would add an additional mask layer without deleting the present layer first.
4. Implemented new semi-automatic Kidney Segmentation (3D from T1). It is based on EdgeWave Live semi-automatic approach.  Constraints are specified instead of Blanket.

EdgeWave Live with CONSTRAINTS kidney segmentation:
Completely Seedless processing is available now.  To view the prototype In present interface we simply set   SIlow\SIhigh = (0.1,100).  Then we just set the appropriate Edge threshold by dragging the slide bar.

SiLow\SiHi are set to INCLUDE ALL.  The only parameter to update is the Edge threshold.

Implemented new semi-automatic Kidney Segmentation (3D from T1). It is based on EdgeWave Live semi-automatic approach.  Constraints are specified instead of Blanket. Generally only 2 slices require user to draw Start and End constraint.

A19 (coronal):  User specifies   Start and End constraint stroke.

User call    MainMenu>ROI>Morph Convex to construct full constraint.

User calls   Applications>CERENE3D>T1: Segment Kidney with Constraint