Checking a potential problem in PERFUSION datasets.  There seem to be dark frames included at regular intervals in the dataset.  Is this OK?

Cleared the renal single slice registration dataset that was not registering well before, great registration quality.  Screenshot shows registration of Target ROI to one of the following timepoints (#8) that was not registered well before.

AutoFocus registration (SingleSlice volumes):  corrected defect when constructing Target operand with Downscale>1.

Single slice registration 3D\4D:   fixed defect when URAL\URALTAU measure would not work.  Defect was in improperly cleaning the margins of the gradient map in 2D case (whole map was set to 0).

4D registration of a single slice Renal volume (CIR):  corrected defect that produced the message "Incorrect Isotropic resolution".

MainMenu>3D Projection>{Make Isotropic,Rotate and Create New volume} functions.  Fixed defect when the function would run but resulting document would not be created.

FireVoxel Build 190 is released.

1. CERENE3D workflow Menu:  added "T1: Segment Kidney  {BLANKET,CONSTR}" items.
2. Breast lesion workflow:  corrected the defect in   PET->T1 registration when the SI volume has to be specifically Active resulting in the warning message
3. Dialog EdgeWaveLive: fixed the defect when changing one of the "Live parameters" would add an additional mask layer without deleting the present layer first.
4. Implemented new semi-automatic Kidney Segmentation (3D from T1). It is based on EdgeWave Live semi-automatic approach.  Constraints are specified instead of Blanket.

EdgeWave Live with CONSTRAINTS kidney segmentation:
Completely Seedless processing is available now.  To view the prototype In present interface we simply set   SIlow\SIhigh = (0.1,100).  Then we just set the appropriate Edge threshold by dragging the slide bar.

SiLow\SiHi are set to INCLUDE ALL.  The only parameter to update is the Edge threshold.

Implemented new semi-automatic Kidney Segmentation (3D from T1). It is based on EdgeWave Live semi-automatic approach.  Constraints are specified instead of Blanket. Generally only 2 slices require user to draw Start and End constraint.

A19 (coronal):  User specifies   Start and End constraint stroke.

User call    MainMenu>ROI>Morph Convex to construct full constraint.

User calls   Applications>CERENE3D>T1: Segment Kidney with Constraint

Dialog EdgeWaveLive: fixed the defect when changing one of the "Live parameters" would add an additional mask layer without deleting the present layer first.

Breast lesion workflow:  corrected the defect in   PET->T1 registration when the SI volume has to be specifically Active resulting in the warning message.  Now any layer can be active before the operation.

CERENE3D workflow Menu:  added "T1: Segment Kidney  {BLANKET,CONSTR}" items. 
Added a place holder for the automatic kidney seed detection.

Build 189A is released.

Fixed the crash defect in 4D->3D slice-by-slice registration with Target ROI.

FireVoxel Build 189 is released:

1. AutoFocus4D dialog box:  corrected a crash defect due to unsupported even handler after removing the SliceMode combo box.
2.Breast lesion registration:  updated default registration parameter to accomodate a requirement that a precise (not overinclusive) lesion ROIs would be provided.
3. AutoFocus3D\AutoFocus4D providded separate allowance intervals for each of the axis {x,y,z}.
4. PET-FDG Motion correction:  increase speed by x10+ times.  This is base on the observation that gross motion is usually due to the "Turning of the head" rather than "Tilting" during exam.
5. "Small" vs. "Large" motion correction options were eliminated and folded into one single Motion Correction
6. PET motion correction:  modified default parameters to increase the search range for better registration quality without any speed penalty (compensated by choosing smaller radius in the URAL feature detector).
7. 3D->3D,4D->3D} slice-by-slice registration:  implemented option for the current timepoint of source to be used to calculate a single transformation for all timepoints. Integrated this new functionality into the Breast lesion registration workflow.
8. "Layer Control Dialog> Load DICOM layer" :  fixed the defect  crash defect when "Load DICOM" button is pressed.
9. AutoBuild Test added subtests for:  DialogAutoFocus3D, DialogAutoFocus4D, EPI->T1 registration in Breast lesion workflow, for the automatic segmenation of Blood Vessel map, CERENE3D  kidney perfusion coregistration.
10. Breast lesion workflow:  added functionality and user interface to register PET-3D volumes to T1-3D volumes.

Auto Build Test:   added subtest for CERENE3D  kidney perfusion coregistration.

AutoBuild Test:  restored the subtest for the automatic segmenation of Blood Vessel map.

Breast lesion workflow:  added functionality and user interface to register PET-3D volumes to T1-3D volumes.

AutoBuild Test: added subtest for EPI->T1 registration in Breast lesion workflow.

AutoBuild Test:  added subtests for  DialogAutoFocus3D  and DialogAutoFocus4D.

"Layer Control Dialog> Load DICOM layer" :  fixed the defect  crash defect when "Load DICOM" button is pressed.

{3D->3D,4D->3D} slice-by-slice registration:  implemented option for the current timepoint of source to be used to calculate a single transformation for all timepoints.

Integrated this new functionality into the Breast lesion registration workflow.

PET motion correction:  modified default parameters to increase the search range for better registration quality without any speed penalty (compensated by choosing smaller radius in the URAL feature detector).

PET-FDG Motion correction:  increase speed by x10+ times.  This is base on the observation that gross motion is usually due to the "Turning of the head" rather than "Tilting" during exam.  New FireVoxel functionality was used that allowed to set separate Max Rotation angle intervals for each axis.

"Small" vs. "Large" motion correction options were eliminated and folded into one single Motion Correction.

4D Kidney registration, case nucs05.  This is a large rotation (12+ deg) case.  Default registration parameters (max rotation) were increased to capture large rotation.  New feature of separate Max Rotation angles for each axis has allowed not to increase processing time.

Registration on the timepoint of the extreme rotation.

Here is the processing result in (.FVX)
https://drive.google.com/file/d/0B2lI9iEKOqv6UVFGclppVUEzWEE/view?usp=sharing

AutoFocus3D\AutoFocus4D providing separate allowance intervals for each of the axis {x,y,z}.  This would potentially allow to achieve  high speed gain in registration by selecting only some axis where the principal rotation occurs.

Breast lesion registration:  updated default registration parameter to accomodate a requirement that a precise (not overinclusive) lesion ROIs would be provided.

AutoFocus4D dialog box:  corrected a crash defect due to unsupported even handler after removing the SliceMode combo box,

FireVoxel build 188 is released.

1. Developed command line interface and *.exe module to access all the functionality of the Dynamic Modelling module.

2. DicomOpen dialog box: corrected crash when STUDY item is selected and attempted to load.

3.DICOM Open dialog box:  combined 2 buttons for loading 4D volumes into a single  "Load 4D" button.  This replaces "Load Siblings" and "Load Range 4D" buttons.

4. 3D\4D registration and corresponding dialogs - allow individual axis of Autofocus to have separate MaxScale values.  This would allow to address registratios with the individual axis distortion (f.e. dr. Sigmund`s  PET-MR registration problem)

5. AutoFocus4D registration:  Reduced SliceMode option to  checkbox Mode2D. Moved this option to the MEASURE panel.

6.AutoFocus4D dialog box:  encapsulated the dialog header into the code file and exposed the global function for calling the dialog.

7.Implemented standalone User-level function "Register AutoFocus3D slice-by-slice"

8. Register by DICOM tags only:  implemented an option when user is asked to present result as the new layer or create an entirely new document.

9. Completely removed the 2D mode option from the Register 3D autofocus dialog box, since this function is a standalone at User-level.
10. Register 4D Autofocus,  "2D Mode" option is now an attribute of the VA_AF4D structure.

11. Removed the redundant "Correct orientation" checkbox from the Register Autofocus 3D dialog box.

12. Workflow breast lesion registration:  implemented a 1-click function to register EPI-4D volume to the T1-3D  volume.  Provided both {with ROI clip,no Roi clip} variants.

Workflow breast lesion registration:  implemented a 1-click function to register EPI-4D volume to the T1-3D  volume.  Provided both {with ROI clip,no Roi clip} variants.

specialized workflow menu

registered EPI lesion overlaid semi-transparent over the T1

Removed the redundant "Correct orientation" checkbox from the Register Autofocus 3D dialog box.

Completely removed the 2D mode option from the Register 3D autofocus dialog box, since this function is a standalone at User-level.

Register 4D Autofocus,  "2D Mode" option is now an attribute of the VA_AF4D structure.

Register by DICOM tags only:  implemented an option when user is asked to present result as the new layer or create an entirely new document.

Implemented standalone User-level function "Register AutoFocus3D slice-by-slice"

AutoFocus4D dialog box:  encapsulated the dialog header into the code file and exposed the global function for calling the dialog.

AutoFocus4D registration:  Reduced SliceMode option to  checkbox Mode2D. Moved this option to the MEASURE panel.

3D\4D registration and corresponding dialogs - allow individual axis of Autofocus to have separate MaxScale values.  This would allow to address registratios with the individual axis distortion (f.e. dr. Sigmund`s  PET-MR registration problem)

DICOM Open dialog box:  combined 2 buttons for loading 4D volumes into a single  "Load 4D" button.  This replaces "Load Siblings" and "Load Range 4D" buttons.

DicomOpen dialog box: corrected crash when STUDY item is selected and attempted to load.

Developed command line interface and *.exe module to access all the functionality of the Dynamic Modelling module.

Provided additional options for deleting Vector ROIs (landmarks).

Added a small "Landmark\Vroi debugging tool".  Under MainMenu>ROI>List All Vector ROIs command.  Would show the list of all landmarks, with their corresponding time intervals and whether they are visible or invisible.

Restored the Automatic Build Test for the Model (34) "Sokoloff  using long formula"

Update the ABT test for "Sokoloff - short formula model".
For PET processing, added new logic - if user specifies the concentration conversion other than "Signal Values" - information dialog box pops up informing the user.  Then Signal is used for Concentration of Input function

Verified basic operation of the "T1-mapping using inversion recovery" model on the small phantom data.  "Modulus (1)" sub-method was used.

Upgraded the "AATH" to the new optimization approach:  Model calculation are performed by User-specified method.  Residual function estimates in terms of the original signal.

Restored the ABT subtest for this model.

Upgraded the "Modified Tofts model" {Ktrans,Ve,Va} to the new optimization approach:  Model calculation are performed by User-specified method.  Residual function estimates in terms of the original signal.
Restored the ABT subtest for this model.

Upgraded Tofts model {Ktrans,Ve} to the new optimization approach:  Model calculation are performed by User-specified method.  Residual function estimates in terms of the original signal.
Restored the ABT subtest for this model.

Restored the Automatic Build Test for models  {0,1,3}

Dynamic Modelling module "Process ROI as a single TAC" mode:  fixed interesting defect for all the models.  There was some undesirable "double->integer" conversion performed on the averaged ROI TAC.  So there was precision lost 0.5 units of signal on average.  Now fixed and is precise.

IN PROGRESS:   Verifying each individual Dynamic Model to work properly with the new Concentration Conversion mechanism.  Regenerating the ABT dataset

Upgraded APIs (application programming interface) to the Dynamic Experiment library so that  Callback functions for Signal->Concentration and Concentration->Signal are supplied for each model calculation.  This would allow each individual model perform fitting of the data in signal units instead of the concentration units.

Updated the design and layout of Dynamic Modelling dialog box
The Input Function view panel is removed.  Instead user can see the Input functions by
pressing the View button.  Then panel displaying all the concentration curves will appear.

Modified and enabled the ViewTac dialog to use the new mechanism of ConcentrationConversion.

Re-engineered the RoiStats4D dialog box. Ensured correct operation with the new Concentration Conversion design.

Finished initial implementation of consistent Concentration Conversion models through the entire FireVoxel.  Concentration conversion is now controlled by 2 dialogs:  "Concentration Method" dialog and the "ROI attributes" dialog.

The following dialogs had their User Interface updated:

1) ViewTac dialog
2) RoiStats4D dialog
3) Dynamic Modelling dialog box
4) Layer Control dialog box

Added a "Tissue Property" attribute to all ROI entities. At the moment this Properties contain only T1 value and will be used in concentration and other calculations.

In the following versions of FireVoxel these Tissue properties will be recorded in the *.fvx file

Implemented a general "Tissue Properties" dialog to be used during the concentration conversion.

New layout and logic of the Concentration Conversion dialog box:



a) All methods are now grouped under the "Method" Combo box

When the specific method is selected, only the relevant fields will be live while others will be grayed and disabled.

New simple redesign of Dynamic Processing dialog:
Note  changes
a) Concentration checkbox is removed from the "Input Function panel"
b) Concentration methods would be extended by a trivial "Use the Curve values" method.
c) Tissue concentration button is added.
d) When the model is selected that does not allow concentration conversion (f.e. PET models), the
concentration button(s) will be greyed.

BPD dataset is fully processed (8 normal + 9 bpd).
Below are full BiCal results (average improvement over N3 is    4.42 times with better WM\GM contrast)

Corrected the defect for "Save File" operations of any kind:  checking the overwrite of the existing file and warning the user.

RoiStat3D\RoiStat4D dialog:  when the volume without raster or vector ROIs is chosen, temporarily create a whole volume ROI and perform the measurement on it.

Implemented Non-uniformity layer measurement (Volume+2 blob layers) function feature:  for each slice number of blobs is measured and difference reported if any.  This helps to quickly find the slices where mistakes are made.

FireVoxel Build 185 is released.

CERENE GFR processing:  When any of the model calculations are activated, the Concentration Conversion dialog box pops up.   By default concentration Method is FWTE.  The TR and Flip angle are entered from DICOM header.  User needs to enter tissue T1 (sec).  AIF (blood) T1 is fixed at the moment and = 1.664 sec.

FireVoxel Build 184 is released.

1. Dialog RoiStats4D:  expanded and corrected functionality so that Raster and Vector ROI could be mixed together. Crash defect on PET-4D is corrected.

2. User Options dialog box: restored proper functioning of the Temp Directory browse button.

3. Removed the "MIDAS-Save" relater options from the User Options dialog box.

4.Upon FireVoxel start, program checks if the "Temporary File folder" specified in User Options configuration file is present.  If it is not present, Temporary file folder is created at default location: ApplicationDirectory:\Temp.
If the above fails, user is advised to reinstall FireVoxel to a different folder or "Run as Administrator" and program terminates.

5. Provided additional system diagnostics when the parametric map files are written.

6. Dynamic Modelling functionlity: moved all the interfacing functions from the main GUI application down to the DLL. This is in preparation to FirevoxelDynamicModellingCurve.exe command line module.

7. NIFTI  Float32 subtype:  enabled the loading.

8. Dialog RoiStats4D: changed the text of the “automatic retile” checkbox.

Dialog RoiStats4D:  expanded and corrected functionality so that Raster and Vector ROI could be mixed together. Crash defect on PET-4D is corrected.

User Options dialog box: restored proper functioning of the Temp Directory browse button.

Removed the "MIDAS-Save" relater options from the User Options dialog box.

Upon FireVoxel start, program checks if the "Temporary File folder" specified in User Options configuration file is present.  If it is not present, Temporary file folder is created at default location:
ApplicationDirectory:\Temp.
If the above fails, user is advised to reinstall FireVoxel to a different folder or "Run as Administrator" and program terminates.

Provided additional system diagnostics when the parametric map files are written.

Dynamic Modelling functionlity: moved all the interfacing functions from the main GUI application down to the DLL. This is in preparation to FirevoxelDynamicModellingCurve.exe command line module.

NIFTI  Float32 subtype:  enabled the loading.

AutoFocus registration with the initial transform: restored to working condition.

Fixed the polynomial transform reslicing problem.

VTF file format read: Added the diagnostic to identify if user tries to load the old VTF format which is no longer supported and displays the suggestion to the user.

Disabled Huffman compression of large REAL volumes with MaxVoxVal>1M, so for major
speed up in saving and loading.

Incorporated support for ANALYZE 32-bit float files.

BiCal non-uniformity correction Dialog is further simplified and optimized:

Numerous improvement to BiCal algorithm:
1. parallelization with about 20% further speed up
2. Another 20% NU improvement on BPD dataset

BiCal Non-uniformity correction:  resolved an issue when simply applying Bias Field correction to the Air voxels would amplify the noise.  New algorithm intelligently corrects transition from Air to tissue so the effective field remains smooth. The non-unifomity correction improvement in the tissue is identical for both variants.

Simple Field application makes the noise amplified.

Intelligent processing of Tissue-to-Air transition

Restore core functionality inside the ROI Wave distance functions based on voxel morphology.

case RE:  difference between "Image matrix center alignment" and "Dicom-tag based alignment"

DICOM tag-based alignment. Complete mismatch of DICOM tags

Image center based alignment, close enough.

Suitable parameters for PET4D-MR4D registration "WITHOUT DICOM alignment"

case RE:   PET4D-MR4D registration

Coronal artery AIF at 1.2 sec time resolution

Dialog RoiStat4D:  when concentration method change the Curve panel should immediately redraw now to reflect new settings.

Kidney AIF experiment: segmentation and concentration from NUFFT.

AIF ROI was automatically sampled using IDIF (~4000 voxels)

Corresponding signal for the AIF

Basic linear Concentration (S/S0-1)  (Conc max = 9.94)

FTWE concentration with actual T1\TR\Flip Angle values  (Conc max=3.50)

Further optimized and streamlined BiCal dialog User interface.  This is the final form for ISMRM.

BiCal: changed the order of  resolution change and NU field application to reduce the blurring of the resulting volume.

a) New result                                             b) Old result

BiCal: fixed numerous memory leaks.

Various concentration models were compared for the GRASP and NUFFT carotid artery curves.

Both curves were provided as *.txt file in FireVoxel TAC format.  Upon opening FireVoxel (no document present) user choose  "MainMenu>Applications>Convert TAC to Concentration"

After choosing the file name, the ViewTac dialog appears with the original GRASP curve

General Concentration conversion dialog box will appear.  User selects the FTWE concentration model.
The core model is:  S = M0*sin(alpha)* ((1-exp(-TR/T1(c )) / (1-cos(alpha)*exp(-TR/T1(c ))

Optionally (with T2* checkbox) the T2* effect could be accounted for, with the following formula

S = M0*sin(alpha)* ((1-exp(-TR/T1(c )) / (1-cos(alpha)*exp(-TR/T1( c)))*exp(-TE/T2*(c))

We start with loading the Carotid AIF file obtained from GRASP:

original Curve from GRASP

After applying the basic FTWE model we obtain this curve

GRASP FTWE (Max Concentration 0.2944)

 Next we enable the FTWE with the T2* effect

GRASP  FTWE with T2* effect (Max concentration 17.94)

In the next part of the experiment we load with the NUFFT curve.  This AIF was obtained automatically with FireVoxel-IDIF function and the ROI size was about 2000 voxels.

NUFFT original curve

After applying the basic FTWE model we obtain this concentration curve

FTWE model, max Concentration = 1.71

  Next we enable the FTWE with the T2* effect:

FTWE model with T2* effect, max concentration = 19.9




CONCLUSION:
NUFFT with FTWE model seem to provide best result with more realistic concentration values. But further evaluations are required.

Dialog ViewTac implemented numerous fixes including

a) fixed the proper display of MaxSignal and MaxTime fields.
b) Removed "Blood vessel" checkbox.
c) Repaired connection to the "Concentration Method" dialog box.

Dialog "ROI Stats 4D":  upgraded concentration handling to the unified concentration dialog box.

Added the "Load TAC folder" field to the User Options, so the current folder is remembered within and between the sessions.

FireVoxel Build 182 is released.

CERENE3D menu:  added new variants for kidney registration
{MI-RAD,MI-ENSEMBLE,URALTAU-RAD} for the further investigation of most suitable algorithm.