FireVoxel Build 166 is released

Download link:

https://drive.google.com/file/d/0B2lI9iEKOqv6eG9nQ0xGazlIdjA/view?usp=sharing

VA grant batch processing dialog, latest version:

Corrected the dialog logic (pasting appropriate dz suggestion) inside the Dialog SpecifyResolution.

DICOM Save:  changed the default compression mode to "Uncompressed".  Enabled load of the result by ImageJ (requires uncompressed).

DICOM File Save:  added tags that were missing in previous versions:
TAG_SERIES_NUMBER
TAG_INSTANCE_NUMBER (former TAG_IMAGE_NUMBER)
TAG_MODALITY

HL-case:  PET-FDG.   Reconstruction artefact due to the Gross motion between timepoints #34 and #36.  It appears that at T#35 the reconstruction has combined the head signal from several grossly distant positions, resulting in blurred image and halo (well visible on left-top corner T#35).
This timepoint is too blurred to be motion corrected but result is reasonable. Everything else is motion corrected quite well.

HL - T#34 (2440 sec)

HL-T#35 (2740 sec)

HL- T#36 (3040 sec)

Comparison of   "IVIM- free fit" on the sample dataset obtained from Henry:  Eric's vs. FVX

Eric's IVIM-free fit.  Residual = 2.33

FireVoxel IVIM-free fit.  Residual=2.006

Comparison of   "IVIM-segmented fit" on the sample dataset obtained from Henry:  Eric's vs. FVX

Eric's IVIM-segmented fit.  M0=Tac[b0].  Residual = 2.3

FireVoxel IVIM-segmented fit.  M0 is fitted.  Residual=2.13

PET-FDG motion correction.  Most challenging case (MB-15) of the last batch.  Before and after motion correction, reference BrainMask from the last timepoint (#38) is overlaid on the maximum displacement timepoint (#27)

Before

After

MainMenu>ROI>Clip Volume by ROI:   completely parallelized the implementation with great performance gain (on long 4D sequences).

FireVoxel Build 165 is released.

Download at:  https://drive.google.com/file/d/0B2lI9iEKOqv6RE1sSno1a19yc00/view?usp=sharing

1. FireVoxel file save - disabled the PHI warning,

2. Fixed crash defect:  4D volume overlaid by 3D-ROI as active layer.  Calling EdgeWave function was producing crash.

3. Defect fix: EdgeWave algorithm on real-valued volumes:  provided correct conversion of units from the dialog box to the actual procedure.

4. Affine transform reslicing: substantially increased the parallelization resulting in about x2 speed improvement on the developmental 6-core platform.

5. SIG_DIFF registration measure:  changed accumulation from L2 to L1 norm.

6. UI - VolumeSmooth function:  Removed erroneous  "ROI required function"

7. VolumeSmooth (Median):  corrected the fixed memory allocation for the sorting, so the smoothing of double-valued volumes does not crash anymore.

8. Fully parallelized the VolumeSmooth procedure so it runs with the 100% load on 12-thread system.

9. Implemented initial variant of the "DICOM File Extractor" dialog box.

Implemented initial variant of the "DICOM File Extractor" dialog box.

Next iteration of CT file extractor dialog:

Initial Prototype of CT DICOM file extractor for VA grant.

Fully parallelized the VolumeSmooth procedure so it runs with the 100% load on 12-thread system.

VolumeSmooth (Median):  corrected the fixed memory allocation for the sorting, so the smoothing of double-valued volumes does not crash anymore.

UI - VolumeSmooth function:  Removed erroneous  "ROI required function"

DICOM Tree functionality:  decoupling the DICOM volume objectification functionality from the DICOM-Folder-Tree dialog box.  This is so that functionality could be used by other DICOM-related dialogs.

Register 4D volume to 3D:  major code re-engineering.

Registration of 3D/4D volume to ROI.  This frequent and useful scenario is greatly sped up by adding the "Target ROI" identical to the binary Target and inflated by 1 voxels. This improvement is only effective for the URAL-measure scenarios.

SIG_DIFF registration measure:  changed accumulation from L2 to L1 norm.

Affine transform reslicing: substantially increased the parallelization resulting in about x2 speed improvement on the developmental 6-core platform.

Defect fix: EdgeWave algorithm on real-valued volumes:  provided correct conversion of units from the dialog box to the actual procedure.

Fixed crash defect:  4D volume overlaid by 3D-ROI as active layer.  Calling EdgeWave function was producing crash.

FireVoxel file save - disabled the PHI warning, so it is the full user responsibility now.

FireVoxel Build 164 is released.

1. SulciPrint2D:   Added basic skeletonize functionality to binary SulciPrint2D.

2. MainMenu>Volume>Pad:  added the function to pad\extend volume with "0" fringes of the specified size (in mm).

3. BiCal post ISMRM follow-up and corrections.  Introduction of the new BiCal version - Multipass. Original BiCal is rebranded "BiCal Basic" on the user interface.  BiCal Multipass becomes "BiCal" on the user interface.

4. Corrected the cleanup of the FireVoxel working directory upon start\close of the Application.

5.Completely new BiCal algorithm is introduced with greatly simplified interface.

5. Included additional heuristics into the loading logic of the MIDAS  *.time files to correct the reported loading defect.

6. FireVoxel ABT: for each of the time-based dynamic model added an option to run the test both for the FVX file format and MIDAS file format.  Three actual models are verified in this dual mode.

7. Corrected: when in a 3 or more layer volumetric entity, the ROI is selected and the other layers are SI-volumes, a crash occurs right after the "Ambiguous layer configuration" message.

8. All Dynamic parametric models:  non-functioning "Process All" option was restored.

9. F9 function key brings up the FVX "Save Document" dialog box.

F9 function key brings up the FVX "Save Document" dialog box.

All Dynamic parametric models:  non-functioning "Process All" option was restored.

Corrected: when in a 3 or more layer volumetric entity, the ROI is selected and the other layers are SI-volumes, a crash occurs right after the "Ambiguous layer configuration" message.

FireVoxel ABT: for each of the time-based dynamic model added an option to run the test both for the FVX file format and MIDAS file format.  Three actual models are verified in this dual mode.

Included additional heuristics into the loading logic of the MIDAS  *.time files to correct the reported loading defect.

BICAL parameter dialog box:
Reduced and greatly simplified and reduce # of parameters.
Notice new option: processing without Edge detection.

New generation of the BiCal algorithm is ready => "BiCal Multipass"

Sample of the processing on BPD-001

170 seeds were manually constructed over the White Matter.
Original nonuniformity =  0.608
N3-corrected (2-pass)     =  0.31
BiCal MP                         = 0.057


Both N3 and BiCal preserved the WM\GM contrast measured between close pairs of seeds = 1.67+/-0.24.

ORIGINAL volume:   White Matter Nonuniformity = 0.608

N3-corrected volume (double pass with aggressive FieldSmoothness=10mm):  White Matter non-uniformity = 0.31

BiCal-corrected volume:  White matter non-uniformity is 0.057

BiCal Explorer Classic:  restored the dialog box and processing to find out optimal parameters for BiCal correction.

BiCal dialog processing: 
a) Added the "Enchanced Edge" option corresponding to the URAL-grad to processing.
b) Removed the "Reuse Edge" checkbox option from the interface to ensure it is always on.

Corrected the cleanup of the FireVoxel working directory upon start\close of the Application.

BiCal post ISMRM follow-up and corrections.  Introduction of the new BiCal version - Multipass. Original BiCal is rebranded "BiCal Basic" on the user interface.  BiCal Multipass becomes "BiCal" on the user interface.

MainMenu>Volume>Pad:  added the function to pad\extend volume with "0" fringes of the specified size (in mm).

SulciPrint2D:   Added basic skeletonize functionality to binary SulciPrint2D.

FireVoxel Build 162 is released.

1. Re-engineered the "VolDisplay.cpp"  

2. Implemented the "MainMenu>Projection>Active Layer: Project to single slice volume"

3. Corrected the Layer arithmetic operations  AbsDifference and TruncatedDifference.

4. Layer control dialog:  increased the spacing between the layers name.

5. Added function to measure difference between two SulciPrint2D in Binary Mode.

6. Added function for SulciPrint2D difference in "Depth mode".

7. Added one-step function  "View SulciPrint  (2D\3D) in Binary Mode"

8. Added one step function to view SulciPrint 2D\3D in "Depth mode".

9. Greatly simplified entire "BrainPrint>SulciPrint" workflow putting all the function as ONE-STEP commands under the single menu.

Greatly simplified entire "BrainPrint>SulciPrint" workflow putting all the function as ONE-STEP commands under the single menu.

Added one step function to view SulciPrint 2D\3D in "Depth mode".

Added one-step function  "View SulciPrint  (2D\3D) in Binary Mode"

Added function for SulciPrint2D difference in "Depth mode"

Depth difference map:   units are in 0.01 mm

Added function to measure difference between two SulciPrint2D in Binary Mode.  Measure on the Test-Retest pair, the mismatch is 8% of all surface voxels.