"Deep breathing" lung segmentation case:  no leaks after BiCal+EdgeWave

Some very approximate parameters for BiCal - would work in the wide range.

BiCal parameters

EdgeWave (with seed) parameters

Mouse Brain, CT-PET-ATLAS wokflow:

Provided an additional registration function to register everything to the PET space to avoid any transforms\interpolation of the principal data (PET).

Mouse Brain,  CT-PET-Atlas workflow.



1. Load Atlas once for the whole study session. Minimize the View, so it is out the way and reduce screen clutter. You don't need to open Atlas for every registration.

2.  Load CT-3D volume with landmarks present

3.  Load PET-4D volulume

(steps 2,3 in any order)

4.  Choose "MainMenu>Applications>Mouse Brain Atlas-PET-CT workflow"

5.  After brief processing only one document will remain that contains
CT,PET and several ROI layers.

6.  Press F4 to bring up the curve dialog, this might take up to 1 min since there are many ROIs present.  You will see something like below:

Mouse Brain   CT-PET-Atlas workfow:  finished the integrated "one-click" registration function.  Resulting entity is ready to get the PET curves and save them (to text file)

Prepared first integrated mouse brain Atlas with ROI regions named and the 4 Landmarks included.  This is ready for the final processing.

Added the functionality to extract only desired regions from the Atlas.  User enters the desired region indices separated by commas.  Result: they will appear as the new ROI layes named "atlas region #x" according to the specified indices.

Landmark co-registration:
a) When Source={3D,4D} 2-layer entity, registered to a 3D-volume, the timing information of the 4D volume was lost
b) Also corrected the defect when Alpha (transparency) and the color scheme of the source were lost after the regidstration.

Dialog RoiStats3D:  in Model-based Histogram segmentation added an option to view the "Modelling Cumulative" curve  (options are {None,All Curves,Cumulative"}
Also removed the "BiGauss Explore" and "BiGauss with Ratio Explore" options since they are superceded by the curves display now.

Histogram model-based segmentation {BiGauss,BiLaplace}: Implemented initial framework to show the modelling curves overlaid on top of the histogram. Notice the threshold is chosen as the midpoint between 2 peaks.

Implemented some improvements to Global Optimization algorithm and code.

Verified correct result of Histogram segmentation using "Bigauss with Ratio" method on the sample from EdgeWave manual.  BiGauss ration interval was [1.1,2]. This did not seem to work on Henry's computer.

Fixed crash defect while loading the DICOM folder obtained from Mr. Zhang under Win10. This was due to using the 32-bit truncation in CTreeCtrl::SetItemData during the DICOM tree construction.

Moved the main development environment to Windows 10.

Fixed the defect in RasterPaintbrush dialog box:  checking the "Allow paint on parametric Maps" had no effect and setting was not remembered.  Drawing on Parametric maps is now possible.

Fixed the paintbrush problem when drawing on integer volumes.

Registration by the landmarks:  provided more detailed analysis in case of the landmark mismatch between Source and Target.  List of Source mismatch landmarks + List of Target mismatched landmarks is provided.

Registration by Landmarks:  upon the start of the procedure all the "invisible" (void) landmarks are unconditionally removed from ALL documents. This is to avoid frequent confusion during the registration.

Mouse CT->Atlas landmark registration (suing 4 landmarks).

FireVoxel Build 204 is released.

1. Fixed the SaveDicom defect introduced by the DeIdentifier code.

2. AutoFocus 3D registration: when the Target volume is ROI, allow to use it as a Target ROI role two (so it serves two purposes

3. T1-EPI-PET lesion workflow:  added an option to register the whole lesion ROI at once ("3D Mode").

4. "Dialog RoiStats4D : Save Curve" function:  in case of 4D ROI added information about the volume of the ROI for each timepoint.

5. When dynamic dimension="TIME", we output the time values as a difference from the initial timepoint.

6. EdgeWave resulting layer name generation - improved with adding the name of Dynamic component in case of the 4D volumes.

7. EdgeWave on near-isotropic lung volume "shifted-y-axis" defect:  was caused by slightly different definition of "isotropic" between different software modules.

8. Defect "View Projection of the Selected Entity": fixed defect when specifying projection produced an immediate crash.

Fixed the SaveDicom defect introduced by the DeIdentifier code, so the changeSeriesUID flag was not functioning.