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.

Dialog Split ROI by threshold:  added "%" information for 2 separated segments.

Dialog "ROI split by threshold":  expanded to work with the Parametric maps.

AutoFocus4D   registration dialog box:  fixed the drop-down combo box to expose all the interpolation options during the registration.

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

Liver Blood vessel segmentation.
New method is based on the "Time of Active Rise" technique developed years ago.  This can be applied to any organ in dynamic contrast studies.  "Time of Active Rise" parametric map is constructed and then a single simple threshold is chosen (in seconds).

FireVoxel Build 149 is released.

Download at:
https://drive.google.com/file/d/0B2lI9iEKOqv6N2U0a08taG9ZM2c/edit?usp=sharing



1. Sulci-ROI segmentation:  implemented function "Wave Distance" from the Brain mask ROI surface to its convex hull.
2. Implemented  the Support Module for measuring the Wave Distances in various scenarios.
3. Prototype of Sulci segmentation from  GM-CSF interface.
4. Fixed the crash related to DICOM features:  when volume is transformed with the dimension change (or similar operation),.
5. ABT: new subtest for Rotate+Scale of large volumes with all possible interpolations.
6. Volume Affine transform:  optimized memory usage  and workflow so it is possible to have a destination volume exceeding 1.5 billion voxels. 
7. Volume histogram calculation: optimized the memory workflow so very large volumes could be processed. 
8. DICOM load of very large: optimized memory workflow so no memory failure happens on 1.5 billion voxel volume.
9. Volume Arithmetic operations on very large volumes:  Optimized the memory workflow so the operations do not fail on volumes with upto 1.5 billion voxels timepoint.
10. SIEMENS De-identified DICOM load:  corrected the logic so the 4D dataset could be logically combined and loaded properly.
11. Added User Interface-level functions:
  a)Measure Surface Wave distance to Inside of the ROI
  b)Measure Surface Wave distance to Outside of the ROI

12. Surface Atrophy Depth measurement.  Added User Interface function "MainMenu>Brain>Measure Surface Atrophy depth"

13. Bruker ANALYZE 7.5:  added detection of the signed short integers in ANALYZE file, then offering user an option to treat file as a Bruker ANALYZE 7.5

14. Corrected the loading of ANALYZE-based  (.img)   4D file (.time).

15. MainMenu> {"Open RAW 3D", "Open RAW 4D"} functions:  added functionality so that last used extension is remembered and used as the default next time the dialog opens.

16. Completely re-engineered User Interface and the implementation of the "Aggregate projections"  -  {MIP,Surface}

17. Corrected the UI behavios:  In EdgeWave, if Vol+RoI is present,  ROI is disabled (invisible), but being Active ROI was still chosen as the operand.

18. Parametric Map calculation:  when resulting file is loaded, a check is performed if invalid floating point number is present (INF or NAN), message is  then displayed.

19. Dynamic Parametric Map module:  completely re-engineered the Model-1 ("Variation") and added an ABT validation subtest for this model.

20. Dynamic Parametric Models: Completely re-engineered Model 4 - "Input Function Distance". Added a corresponding ABT validation subtest.
21. Dynamic Parametric Models: Completely re-engineered Model 5 - "Custom Time of Active Rise". Added a corresponding ABT validation subtest.

Dynamic Parametric Models: Completely re-engineered Model 5 - "Custom Time of Active Rise". Added a corresponding ABT validation subtest.

Dynamic Parametric Models: Completely re-engineered Model 4 - "Input Function Distance". Added a corresponding ABT validation subtest.

Dynamic Parametric Map module:  completely re-engineered the Model-1 ("Variation") and added an ABT validation subtest for this model.