BiModal histogram segmentation within the RoiStats3D dialog box.

a) Added the separate "Recompute" button to simplify the processing
b) Currently selected\displayed histogram binning is supplied and used as the distribution for the BiModal modelling.
c) Corrected the Model Curve overlay to be consistent with the change in binning specified by the User.
d) Eliminated the "BiGauss model"  only leaving the "BiGauss with Ratio model".  Just set the very high peak ratio (>10) to get result of the previous models.
e) Fitting Thresholds\Residual are now displayed in the "Threshold" status line.

BiGauss model (residual 57.7)

BiLaplacian model (residual 86.6)

Enabled a correct progress meter inside the Breast-FGT "compounding workflow".

Developed an adaptive function to separate breast image into L&R.  This is to compensate for 2 possible operator related errors:  initial acquisition centering and positioning of the cropping ROI.

BiGauss Histogram modelling (on the ventricles image):
Observation is that the "With Ratio" variant executes much faster than "Without Ratio" variant.
But then on this particular sample  the second one seems to have much better result.

Bimodal Gauss WITH Ratio

Bimodal Gauss (without Ratio)

BiGauss Histogram (without ratio) modelling:  Added the progress bar.

Improved Automatic DICOM loading function (does not require user input). Now function may be supplied with the file folder name. Before it required only the image file name of the actual dicom file.

FireVoxel Build 209 is released.

 1. Fixed the "IM file crash problem" (equal sign was missing):  an appropriate error message would be displayed now.

2. IVIM segmented model:

a) added parameter "Large B-value start" with the default value=200.  User can now change that value.

b) Increased the allowed ranges for Dp=[0,1],  Dt=[0,0.01]

IVIM basic model:

 Increased the allowed ranges for Dp=[0,1],  Dt=[0,0.01]

3. On Mouse Move - Display voxel information:  fixed a defect when the Active Layer is disabled, so moving the mouse did not produce any information in the status line.

Now if the Active is disabled, we choose the First enabled layer to display the voxel info.

4. Synchronize Multiprojection Cursor (mode=ON) functionality:  if there is a single View\Projection of the volume is visible the Crosshair cursor would not be visible.

5.  BiCal on Sodium images: fixed the defect when iterations of BiCal were producing a "better" result. This was due to the custom scheme of processing the REAL images, when internally they were converted to the 15 bit images and this was conflicting with the internal truncation  

Verified "Registration by DICOM-tags" on the PET-MR sample provided.  Matching quality seems to be good.  Since torso is included, it is unlikely any other registration could\should be used.

Fixed the "IM file crash problem" (equal sign was missing):  an appropriate error message would be displayed now.

IVIM segmented model:
a) added parameter "Large B-value start" with the default value=200.  User can now change that value.
b) Increased the allowed ranges for Dp=[0,1],  Dt=[0,0.01]

IVIM basic model:
 Increased the allowed ranges for Dp=[0,1],  Dt=[0,0.01]

"IVIM-Segmented"  model:
We try to investigate a suspicious peak in the histogram of the fitted Dp-parameter.  This peak occurs at Dp=0.03.  In the screenshot below one of such voxels was identified and processed individually.

Green-data curve.  Black - fitted curve.

For finding the Dp component we run the Global Optimization with parameter Dp be restrained to the [0,0.03] interval.  So optimal solution is found to be on the borders of that interval, i.e. Dp= 0.03.
Many such voxels within the ROI contiribute to the "suspicious peak".

The problem does not seem to be restricted to the cases of air/tissue partial voxels.
My current guess that this is common to the voxels where signal curve is not monotonous.

Here is anther case with Dp=0.03

Next experiment, I vastly increased the Dp-constraint interval to [0,1] and ran it on the same voxel.  Interestingly the result has settled on Dp=0.67 with 3 times lower residual.  This indicates that we have found an actual optimum.

Fit with Dp=[0,1] allowence. This settled at Dp=0.67

CONCLUSION:  seems like the presence of the  Dp- histogram tail peak is due to the restriction of the Dp=[0,0.03] during the optimization.  I will be relaxing this restriction to Dp=[0,1].
My best guess that the "presence of the histogram tail peak" is not related or causing the difference of the results with other software.  I use the Global Optimization which is very different from Local Optimization used in other software.  To my best knowledge the FireVoxel fits are valid and excellent (judging by the residual). So my best guess is that "other software" is not fitting well enough.

Here is the histogram of resulting Dp values with  Dp=[0,1].  Previous strong peak at Dp=0.03 is gone. My best guess: these high values due to some voxels having strongly monoexponential signal
curve.

We can get to the bottom of it if I send a single Signal Curve, along with FireVoxel-calculated parameters and residual.  Then curve can be processed in "other software", residuals compared and so on.

On Mouse Move - Display voxel information:  fixed a defect when the Active Layer is disabled, so moving the mouse did not produce any information in the status line.
Now if the Active is disabled, we choose the First enabled layer to display the voxel info.

Synchronize Multiprojection Cursor (mode=ON) functionality:  if there is a single View\Projection of the volume is visible the Crosshair cursor would not be visible.

BuiCal nonuniformity correction over the set of 12 "Sodium"-images.

To precisely evaluate the effect of the correction, 15-20 seeds were precisely and manually constructed on each of the cases.  All of the seeds were positioned inside of the ventricles as far as possible from the edge of ventricles and corresponding partial volume voxels.

Non-uniformity is defined as the StdDev of the average seed signal taken over all the seeds.

Seeds are in Red on one of the slices 

We tried to find set of parameters that worked well on every single image.

See the Table of results below for each case  

1st column:  Case name

2nd Column:  original non-uniformity (StdDev over seeds)

3rd Column: processed non-uniformity (StdDev over seeds)

5th column relative improvement of the correction =NUbefore/NUafter-1

Interestingly the results for N-cases where 10 times weaker than the results on "Non-N cases", 6% and 61% improvement correspondingly.

N3 correction was attempted but NU only worsened with all the parameter combinations we tried.

Overall these images are quite challenging for Non-uniformity correction, due to the low resolution and the ventricles being only 3-4 voxels thick.  Note the original .NII files contained the resolution of (1,1,1)mm but this does not seem to be the case,

BiCal on Sodium images: fixed the defect when iterations of BiCal were producing a "better" result.
This was due to the custom scheme of processing the REAL images, when internally they were converted to the 15 bit images and this was conflicting with the internal truncation mechanism after the correction.

Sodium image for testing the BiCal non-uniformity correction.  NII file resolution is listed at 1mm^3 (dimensions are 128x128x128) but it seems incorrect.  User desire the signal in ventricals (see the seeds) to be uniform.

Build 208   is released.

1. IDIF function: Fixed the "invalid rectangle" defect exhibited on P1.fvx.  This was due to the inflated initial rectangle to be outside the image bounds.

2. Implemented an order-of-magnitude CountBits( PBYTE Array,int Start,int End) function which is frequently used throughout.

3. Dynamic Modelling (models {0,3}): fixed the user defined parameters for starting dynamic index to 1 (from 0).

4. Dynamic Modelling framework fix:  When PET image is processed with "Process ALL", i.e. without the ROI, the dialog box was popping up asking to specify T1.

5. Dynamic Modelling:  added a test for Tissue Concentration if the Modality=PET. In this case the Concentration Method is always set to "SIGNAL" and user is warned.  This is done in addition to an earlier implemented check for the Input Function in PET.

6. Dynamic Model "Input function correlation": Added a proper handling of the Tissue concentration. Before it was "Signal only" and created inconsistencies for the user.

7. Dialog Layer Operations: fixed crash defect related to the Entity Layer upgrade to 22 layers in the previous builds.

8. Fixed the error in reslicing binary volumes (ROIs).  Old procedure was always assuming the FillVoid or Background value is always '0' but this is not correct always.  This was detected in "Reslice Target to Source" option during the Femur registration.

9. Dynamic Modelling:  Input Function correlation: corrected the situation when the divisor n*XX-X*X or n*YY-Y*Y is close to zero.

10. Dedicated menu item was added to the workflow menu with the parameters suited for processing.

11. LayerControl dialog: updated behavior so that the Name editing requires Doubleclick, while "ROI advance to midslice" requires "Ctrl+Doubleclick".

IDIF function: Fixed the "invalid rectangle" defect exhibited on P1.fvx.  This was due to the inflated initial rectangle to be outside the image bounds.

Implemented an order-of-magnitude CountBits( PBYTE Array,int Start,int End) function which is frequently used throughout.

Dynamic Modelling (models {0,3}): fixed the user defined parameters for starting dynamic index to 1 (from 0).