FireVoxel Build 156 is released.

1. Gradient withing URAL-radius to the Volume boundaries are set to 0 to avoid introducing non-existing features that might steer registration.

2. If one of the timepoints in registration is binary (as sometimes in hybrid scenario), the URAL_NORM=Linear is always chosen for that specific timepoint independent of what norm is specified by the user.

3. MainMenu>Volume>Effective Noise:  corrected the defects, crashes on 4D volumes4. RoiStats3D dialog:  added information about the number of the VOID voxels of the SI-Volume within the specified ROI.

4. Implemented the corrections to the Liver DCDI  4D registration parameters.  

Implemented the corrections to the Liver DCDI  4D registration parameters.  This was to fix example "OV" that had very high contrast enhancement thus failing the registration as high gradient inside the contrast regions were attracting the feature detector.
URAL_UNI measure was employed, with the sigmoid function base of 3*Noise.  Automatic noise detection step was added to the registration.

RoiStats3D dialog:  added information about the number of the VOID voxels of the SI-Volume within the specified ROI.

MainMenu>Volume>Effective Noise:  corrected the defects, crashes on 4D volumes.  Obtain the result on GRASP very similar to the Riccian noise result but without the user specifying the size of the search window.

Added corrections to the general registration algorithm for URAL measure:

a) Gradient withing URAL-radius to the Volume boundaries are set to 0 to avoid
introducing non-existing features that might steer registration.

b) If one of the timepoints in registration is binary (as sometimes in hybrid scenario), the URAL_NORM=Linear is always chosen for that specific timepoint independent of what
norm is specified by the user.

FireVoxel Build 155 is released.

In 3D volume DICOM load, increased the interslice distance tolerance from 1e-4 to 1e-3. This allows to load A.R. volumes without warning messages.

FireVoxel Build 154 is released.

1. Added the BrainCT  workflow (MainMenu>Applications).

Added new function "BrainCT>Segment Intracranial cavity".

2. EdgeWave dialog:  corrected a major UI error.  When no seeds are present, the logic of selecting the Connected Component choices (radiobuttons) was damaged.

3. Corrected interface and initial parameters to process the CT-brain scans without leaks.

4. Toft's model (#8):  re-arranged the optimization variables to improve the solution bounds.

5.  Introduced a “Balanced solution” concept for parametric fitting and Toft’s model in particular.

6. Tofts modified model (k-trans,Ve,Va):  implemented changes to model similar to the regular model.

7. Corrected defect:  Unable to "Crop 4D All Layer" \ "Crop 4D Active Layer" using the vector ROI.

8. Added ABT subtest for "Tofts modified (K-trans,Ve,Va)" model.

9. Fixed major bug in registration of real-valued volumes (=PET).

Fixed major bug in registration of real-valued volumes (=PET).

Added ABT subtest for "Tofts modified (K-trans,Ve,Va)" model.

Corrected defect:  Unable to "Crop 4D All Layer" \ "Crop 4D Active Layer" using the vector ROI.

Tofts modified model (k-trans,Ve,Va):  implemented changes to model similar to the regular model.

Tofts model (but general issue important to all models, incl. Eric's IVIM), this problem originated in Henry's report of very high Ve (>18000) in particular ROI fit.

During the parameter fitting, there might be numerous solutions (both voxelwise and Single ROI), whose Minimization Cost differ by the miniscule amount (<0.01 in relative terms of Absolute Minimum Cost).

We "Balance" the solution by considering all such solutions equally valid candidates.  Then several logics could apply.

Below is the result of one such "Balanced" solution, on the same AATH dataset.  Note, the balancing is done on the level of the single voxel without taking neighboring voxels into account.

New Option is added to the Parmetric Model processing:  "Balance Solution" - ON\OFF.

K-trans (regular)

K-trans (Balanced)

Ve (regular)

Ve (Balanced)

Residual (regular)

Residual (Balanced)

Toft's model (#8):  re-arranged the optimization variables to improve the solution bounds
old: (Ktrans,kep)   -> new: (Ktrans,Ve).  Since user supplies the Bounds for Ve, the calculation
of bounds for  the derived kep = Ktrans/Ve was introducing too big of the interval.

Corrected interface and initial parameters to process the CT-brain scans without leaks.

EdgeWave dialog:  corrected a major UI error.  When no seeds are present, the logic of selecting the Connected Component choices (radiobuttons) was damaged.

Added the BrainCT  workflow (MainMenu>Applications).
Added new function "BrainCT>Segment Intracranial cavity"

FireVoxel Build 153 is released.

Code work and maintenance eliminating the procedure handling 24-bit signal representations.

FireVoxel Build 152 is released.

1. Corrected the defect:  when new document & file are created as a result
of the operation, the document file name may exceed 256 characters which is
the MFC limit for VisualC++ 2010.
2.  Implemented the Registration by DICOM tags only.
3.  Completely re-engineered the AATH model.
4.  Added the ABT subtest for the AATH model.
5. Added the ABT subtest for Blood vessel segmentation.

Added the ABT subtest for Blood vessel segmentation.

Added the ABT subtest for the AATH model.

Completely re-engineered the AATH model.  Fully parallel implementation on a single TAC level.
Implementation is fast enough to process large ROIs in voxelwise manner.

"Register by DICOM-tags only" function is tested on PET-MR.

Corrected a flaw in constructing internal info on  "Image_Orientation_Patient".

Registration by DICOM tags only.  Preliminary result.   S->D and D->S.  4D->3D is tested too.

Another look at the Portal Vein residual (possible) movement after the registration.  Part of portal vein was manually drawn on 6 slices of the initial timepoints.  Corresponding TAC (VIF) was generated.  If there would be a substantial movement out of plane for the PV, we would have observed  sharp iregularities in this TAC.  However, beside one bump in the last quater the curve is very smooth which indicates that PV majorly remains in the same position.

Corrected the effect:  when new document & file are created as a result of the operation, the document file name may exceed 256 characters which is the MFC limit for VisualC++ 2010.

Liver 4D registration:  Liver ROI could be clipped to exclude the areas outside the liver from the consideration.  There is a x10 time smaller files size (66MB vs  660MBs)

FireVoxel Build 151 is released:

https://drive.google.com/file/d/0B2lI9iEKOqv6bHEyVlFwY2MybUU/edit?usp=sharing

1.      Modified saving of ROIs to ANALYZE format to allow ImageJ to properly display the ROIs.

2.      Fixed the crash in  "MainMenu>ROI>Convert 3D to 4D" function. This was caused by incorrect creation of the DICOM header for new 4D Roi.

3.      Re-enabled ABT 8 subtest related to registration after the change in the core Autofocus registration.

4.      Mouse DCE (9 timepoint mouse brain axial dataset).  Determined the set of parameters that provides good quality registration and set these parameters as the default under the MainMenu>MouseDCE>Register using URAL.

5.      DCDI workflow:  released 1st version of the complete documentation.

6.      Finalized the DCDI workflow corresponding to the documentation

7.      Fix:  Loading Diffusion datasets with DCMTK (Siemens private b-value tag):  

Loading Diffusion datasets with DCMTK (Siemens private b-value tag):  

VM (value multiplicity) in DCMTK for the VR="OB" is always set to 1, while

it needs to be variable.  This affects the private Siemens tag for B-value

so only the first character is read (i.e.  "4" instead of "400"). 

 provided a general workaround for VR = {OB,UN}

DCDI workflow:  released 1st version of the complete documentation.

Mouse DCE (9 timepoint mouse brain axial dataset).  Determined the set of parameters that provides good quality registration and set these parameters as the default under the MainMenu>MouseDCE>Register using URAL.

Re-enabled ABT 8 subtest related to registration after the change in the core Autofocus registration.

AutoFocus Registration (3D and 4D):  substantially improved the design and implementation of the AutoFocus algorithm when the Target ROI is positioned close to the boundaries of the Volume.

Made additional corrections affecting the Gradient Measure (URAL), to always inflate Target ROI (internally and implicitly) by 1 voxel to account for the   vertice of the lattice vs.  center of the lattice representation of the gradients.

Both changes have resulted in much better registration in Liver DCDI case.

a) before registration on the mid-sagittal slice                               b) after registration

Fixed the crash in  "MainMenu>ROI>Convert 3D to 4D" function. This was caused by incorrect creation of the DICOM header for new 4D Roi.

Modified saving of ROIs to ANALYZE format to map to {0,255} instead of {0,1}.  This allows ImageJ to properly display the ROIs.

ImageJ is using an incorrect LUT table when displaying the ROI saved by FireVoxel in .IMG (Analyze 7.5) format.  Change the LUT (in Image J) to display the image properly.
I think it is a poor logic on ImageJ site in selecting the LUT.

FireVoxe Build 150 is released.
download here:
https://drive.google.com/file/d/0B2lI9iEKOqv6ZDhESTJrZ3dHeWM/edit?usp=sharing

1. RoiStats3D dialog box: fixed the crash after closing the dialog.

2. AutoFocus4D   registration dialog box:  fixed the drop-down combo box to expose all the interpolation options during the registration.
3. Dialog "ROI split by threshold":  expanded to work with the Parametric maps.
4. Dialog Split ROI by threshold:  added "%" information for 2 separated segments.
5. Liver DCDI blood vessel segmentation:  finalized the function.  User starts with no parameters, default 20% of the voxels are chosen as a blood vessel.  Then interactive dialog pops up when user can interactively adjust that threshold based
6. Expanded the RoiStats3D dialog, so it could be activated with only ROI present (i.e. no underlying

volume).  This is useful for the ROI morphological evaluations (number of voxels, blobs, etc).

7. ABT:  created a subtest that would test Core dialogs for not crashing.

Added the dialogs to subtest  a)  RoiStat3D  b)  RoiStat4D

ABT:  created a subtest that would test Core dialogs for not crashing.
Added the dialogs to subtest
a)  RoiStat3D
b)  RoiStat4D

Expanded the RoiStats3D dialog, so it could be activated with only ROI present (i.e. no underlying
volume).  This is useful for the ROI morphological evaluations (number of voxels, blobs, etc).

Liver DCDI blood vessel segmentation:  finalized the function.  User starts with no parameters, default 20% of the voxels are chosen as a blood vessel.  Then interactive dialog pops up when user can interactively adjust that threshold based on visual evaluation of "Time-to-Peak" parametric map.