Employing Affine transform further improves the quality of registration.

SK:  t=19, before registration

SK: t=19, after registration

Implemented functionality and User's Interface for Smoothing the binary Volumes (ROIs)

Liver ROIs, semi-manually constructed by drawing the contour on every 2nd slice required further smoothing.

Preliminary result: Substantial registration improvement is achieved on Liver-GRASP-DCDI exam

 First, User contructs a fairly precise "Whole Liver ROI" on a single timepoint (SK,t=25).
This is done by outlining the liver on every 2nd slice and applying Fill&Morph operation (total time=5 min).  This Whole Liver ROI will be used in registration and further liver function evaluation.

ROI contours are manually drawn on Axial projection and simultaneously displayed on Coronal.

Before registration: SK-case, timepoint t=20, and the Target Liver ROI (t=25)

After registration: Anatomy and the Target ROI are aligned.

Parameter set that has been  used.

GRASP-4D:  Liver is clearly separated with the URAL-gradient at rad=4.1.   As usual with fuzzy boundaries the radius has to be chosen large enough.

FireVoxel Build 144 is released.

When saving FVX file  format, all the volumetric layer are checked to contain PHI information.  Is yes, the dialog box pops up that recommends to exit and run the Deidentifier.

Implemented a "De-identification" functionality for the FVX file format.  This is to further improve the protection of PHI.  All the tags minimally related to PHI are completely cleared.
 A single function, without parameters is placed under  MainMenu>File>Deidentify.

Provided initial description of the PET "detect ridges" algorithm.

Restoring Automatic Build Test that was unsynched during the FDG\DEC MERGE workflow development.

Corrected the display of VoidVoxel values in the parametric maps

Corrected "Volume Histogram" and related function to properly process volumes containing the
VOIDVOXEL values.

Good registration result in  ASL to MR-GRASp registration
This requires some preprocessing of GRASP to obtain an accurate BrainMask.

PET workflow: implemented User Interface-level function:  Crop Empty Areas.

Implemented UserInterface-level   "Dynamic Integral" function:

Brain FDG-DCE  merge workflow.  This workflow can be made 100% automatic. 
INPUT:      folder containing DICOM file
OUTPUT:  Single merged FVX file, containing both MR4D and PET4D.

Implemented "Convert Mosaic to Volume" function and tested it on MR-ASL data.

Tested the "Arterial delay" parameter in the GRASP-DCE abdominal.  Setting "Arterial delay" up to 5 sec improves the fit substantially.

Corrected problem, during the Save\Load of the 13-layer registered document to FVX format.
For unknown reasons, an UNICODE  "_fgetts" function was failing (part of VC++).  Was replaced by a FireVoxel_fgetts.

PET-FDG BrainMask,  a variant without filling the holes. Some arbitrary threshold parameters here.

PET-FDG  completely automatic  (approximate) Whole Brain Mask.
Primary purpose is a reliable target ROI for registration\motion correction.  Are there other interesting applications of this technique.

PET-FDG:  enabling the BrainMask\EdgeWave tool for brain extraction.

PET-FDG:   developing automatic function for "Target ROI" detection suitable for the Motion Correction.

Implementing "PET-FDG  motion correction"

Build 142A is released.

Further modified the "Linear Concentration" formula by disallowing the first 2 timepoints being considered a peak.

FireVoxel Build 142 is released.

ViewFilter dialog box is activated on F9.  This allows to easily activate dialog without accessing LayerControl dialog>ViewFilter functionality.

Re-designed ViewFilter dialog box so the color-value scale could be easier incorporated into the screenshot for the publication.

Dialog "Layer Operations": extended to 20 layers. Corresponding crashes are fixed.

FireVoxel Build 141 is released.

Dynamic Averaging function: corrected defect due to the conversion of the Real-volume to 32-bit representation.

Modified the "Linear concentration" formula, to compensate for initial "bright" timepoints.
In patient RE this resulted to Max concentration increasing from 0.005 to 0.03


Modified the RoiStats4D dialog, so that the linear concentration of ROI and fitted model could be displayed overlaid.

MainMenu>ROI>Skeleton:  added UI level function for ROI skeleton detection.  Simplistic algorithm works well in 2D case.  3D case would require new more complex algorithm.

PET brain "Ridge Segmentation" function:   finalized interface and functionality for 2D and 3D cases.  Simplistic skeletonization algorithm that works well in 2D, for some reason is not performing well in 3D and would require more time to integrate more precise 3D skeletonization.
Therefore, due to a limited time available,  "Process slices individually" option is always on in 3D case for the time being.

Initial test of FireVoxel "Detect Ridges" function on brain PET.

Left: FireVoxel                                    Right: drawn by expert.

Implemented 2D ROI volume skeletonization function.

FireVoxel Build 140D is released.

Detected ridges function: corrected defect by enabling processing of 3D volumes.

Modified DlgRoiStats4D dialog when it is used after Parametric map modeling to display  RoiTAC vs. Fitted TAC.  "Show All" option is disabled in this situation.

FireVoxel Build 140C is released.

Fixed the problem with the "Segment Ridges" tool.  Resulting document was using the same name as the original thus failing to load.

FireVoxel Build 140B is released.

Layer control dialog:  layout is modified to accommodate
up to 20 layers.

Layer Control Dialog:  added Layer Name editing functionality.  If user doubleclicks on the Layer Name, the dialog box pops up that allows to specify the name of the layer.

Added the "Detect Bright Ridges" function to the User Interface.

Operating volume - user specified increase in the resolution of the resulting "Ridges".  It is practical experience that skeletons might benefit from the increase in resolution since their width of 1 voxels is used to simulate the objects of 0-thickness.  "Increase resolution coefficient" in practice range from 1 to 3.
Interpolation - specifies the algorithm used in image upscaling.

Background detection is a part of the algorithm.  Background is detected by overall smoothing of the volume.  User has to specify  "Radius (vox)" and the type of the smoothing Kernel.

Output parameter - specifies the result of the processing.
Elevation Map - Signal intensity volume specifying the likelihood that corresponding voxel is a ridge.
Ridge Mask:  Binary ROI representing wide ridges.
Skeleton Mask:  Centerlines of the Ridges represented as binary volumes.

Volume Constrained Smoothing function:  updated and corrected defects to allow a Single Slice volume processing.

Liver DCDI: case DA: whole liver calculation

PET ridges, Test-2.  b) is the Automatically processed, with the blue centerlines that were provided to FireVoxel.

Initial test with the "Ridge detection function".  Dark and Bright ridges are detected separately. In this example, only initial pre-processing for Dark ridges is shown.

"Invert Volume function" - extended function from ROI only, to include SI-volumes and Real volumes.  Moved the corresponding User Interface item to "Main Menu>Volume".

Corrected an "initialized memory" error in all Liver DCDI model variants.  It was leading to "Unsupported color mapping" error message.

For all models, when only some (N starting) timepoints of TAC are fitted, do not display unfitted part of the "Fit" curve as "ALL zeroes".

Also the RMSE calculation is corrected to exclude the "unfitted" timepoints.

Liver DCDI.  Parameter {Flow,Fa,EMTT,Ki} comparison for patients AR and DB.

Liver DCDI: patient DB

Parameters (F,fa,EMTT,Ki)

Updated and re-engineered the Layer Operations dialog to include 14 layers and corrected crash defect present in Build 139.

Liver DCDI, case DB, slice #38

Liver DCDI, patient DB,  whole-liver - single slice,  "ROI as a single TAC" processing:

GRASP-DCE, patient MH,  comparison of K-trans for various ROIs created by Anne

K-trans (1/min)

Using Anne's hand-drawn Using FVX IDF of carotid
ROI (carotid)

1.19 0.84       tu-right
0.97 0.67      co-whitematter-left
0.165                                                 0.11       posttreatment-right                    
1.163 0.80       co-whitematter left
0.463 0.31       tu-brainstem-center
2.62 1.82       co-brainstem
1.62 1.13       suspectmass - left temporal lobe
>4 3.86       co-greymatter-right

GRASP  MR-DCE exam.  There are 9 ROIs here.
The tallest curve corresponds to the artery, with max (linear) concentration 0.4.
Next highest curve is the "grey matter", with the max concentration of 0.13.
White matter curves have max concentration of 0.04.

Liver DCDI:  cases processed with  "ROI as a single TAC"










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Liver DCDI: fa (Arterial fraction) parameter comparison:

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Liver DCDI: Ki parameter comparison:














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<LI>

Liver DCDI: Total Flow parameter comparison:

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Liver DCDI:  EMTT parameter comparison:

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"HOT"-color scheme.  EMTT parameter.

"Blue-Yellow" scheme GRASP Liver DCDI exam, parameter EMTT (sec), sample visualization in recommended by IBM.

GRASP Liver DCDI exam, parameter EMTT (sec), sample visualization in "Rainbow" scheme.

FireVoxel Build 139 is released.

Added the progress messages during the "Smart Downscale" operation.

In parametric map calculation, the parallelism is now limited to the number of logical threads of the processor.

Parametric Model calculation:  implementing the "Time remaining" message during the calculation. This should be very helpful for the length calculations.

Incorporating the SmartDownscale technology into the regular "Rotate Volume"  UI function.  This function is also used for scaling but only employed standard interpolation so far.
Immediate need in this is to generate low resolution volumes suitable to produce parametric maps in DCDI (Hersh).

Processing parametric map on 2 patients, liver DCDI model, for Hersh's presentation and paper.

FireVoxel Build 138B is released.

PET workflow:  combined PET-MR AIF "adjustment" function,  corrected the timings assigned to the resulting curve as they were made relative to the initial T0.

Fixed an interesting long term defect in displaying the values of parametric maps, reported by Riccardo Lattanzi.

Expanded layer control dialog to have upto 14 layers (from 10)

FireVoxel Build 138 is released.

Sokoloff parametric models {long, short formula}:  added an Automatic Build Subtest.

Sokoloff models {Short formula, Long formula}:  added user control parameter  "K1 min".  This is designed so user can set a fixed value for fK1, so that K1min = K1max = fK1
This way the design to calculate the Ktrans from the DCE MRI and then transfer it to the Sokoloff model can be realized.

Open DICOM dialog File Preview:  In Build 137, a defect became apparent when the preview of the DICOM file was all "white".  This is an "uninitialized memory type of error" and might have been presented differently on different systems.

Fixed the problem loading with the DICOM single file provided by Riccardo Lattanzi.
This is unconventional DICOM obtained as a result of image processing

Save RAW dialog box:  added a "state variable" so the last used extension is remembered and offered as a default choice next time when the dialog is opened.

Open RAW dialog box:  added a "state variable" so the last used extension is remembered and offered as a default choice next time when the dialog is opened.

Fixed the ANALYZE file loading problem:  old legacy datatype=132 was present in the header. This is not a part of ANALYZE 7.5 implementation.  So it was added as legacy type and the file is loading now.

FireVoxel Build 137 is released.

Completely Re-engineering K-trans model with 3 parameters {K-trans,Ve,Va}...

Completely re-engineering the 2-parameter K-trans model  {K-trans,Ve}.  Will verify on the MR4D from the PET-MR exam...

Major work finished, re-enabling and verifying the Automatic Build Test after partial phaseout of 24-bit processing.

Zoom-to-Display functionality:  converting internal processing from 24-bit  to 32-bit for simplicity and speed.

MR4D (from combined PET-MR exam):
Verifying the "K-trans model" = {K-trans, Ve}.  Adding a corresponding subtest to ABT....

Registration defect  fixed:  while registering two longitudal MPRAGE images, the registration crashes if one of 3 measures is used:  {SignalDiff, CrossCorrelation, RatioUniformity}


Added the ABT subtest for  sag1.im<->sag4.im registration for 5 additional measures:
  {SignalDiff, CrossCorrelation, RatioUniformity,MI,MI-norm}

Fixed the volume overlay problem, when 2 brain volumes with the resolution difference around
1e-4 were not able to overlay.

PET-MR  registration:  Removing optional  "PET resolution\Best resolution" option as it always to the best resolution now due to the new codec.

Verifying the ABT (automatic build test) due to the changes related to the NN-codec.

Providing the code to maintain the backward compatibility with the older FVX format, which has been updated with the new Codec.

Optimizing memory bandwidth around the single slice voxel CoDec.  Converting 24-bit based voxel  representation to 32-bits.

Fully coded,  Presently debugging the "NN-loseless codec"....  required for Hi-res  PET->MR registration.