For ALL  FireVoxel operations using the Vector ROIs as seeds:  new better logic is implemented.
For when a single seed is required and several seeds are present, Fvx requires a single seed to be
selected and warns otherwise.

Ensure correct functioning of the Anatomy-constrained (tube) IDIF function on the Brookhaven PET data.
In this example, two Macroseeds left and right are placed by User on the branches of the carotid artery.
Algorithm ran twice with identical (default) parameters.

Positioning of both corresponding ROIs are shown on orthogonal projections.

Testing latest Anatomy IDIF function on the PET case from  Brookhaven.  This (along with blood data) will be used to validate the IDIF function.

Performed a better registration for SL patient (based on URAL registration measure, not MI), created a Hybrid document, placed Macroseed for the new IDIF function.  Uploading the document to the SkyDrive.

Finalizing the parameter Dialog Box for the latest   Anatomy Constrained Input Function segmenter.

Specifically for calculating distance of the fit of 2 curves that are sampled at highly uneven intervals:  Implemented the function for L2 integration based distance for two functions F(t) and G(t).  Perform exact integration of 2 piecewise linear functions.

Replace the "goodness of the fit" with the new integration function.  Old function was simply a sum of difference at sampled timepoints that was giving unjust weight to the beginning of the curve were sampling was much more dense.

Corrected defect:   after IDIF is segmented, the TAC dialog pops up and now correctly displays the size of the vessel in (mm3) and appends it to the name of the vessel correctly.

MG tumor patient:   created a well-registered  MR-PET overlay.  Included an easy and well working Macroseed.  Uploading this to SkyDrive along with FireVoxel Build 129A.

Substantially increased quality of the registration of PET to MRI in the new version comparing to the variant of registration used by Anne.  This is for the patient MG.  (old=left, right=Build 129A).
Also, with the respect to "reconstructing  PET with MRI priors", notice a very large angle between MRI and PET in the original data.

And new registration result in multiple projections:

Temporarily disabled the parallel version of Amoeba optimization in the Finetune stage of the registration.  This is until we moved to 64-bit code.  This is due to high memory requirement by
certain registration measures, such as URAL. At 64-bit memory above 3GB (under Win) will be accessible.

FireVoxel Build 129 is released.

Tested new "Anatomy constrained" IDIF function segmenter on the PET dataset provided by Henry.

Dialog ROI Stats 4D (TAC viewing dialog):  removed redundancies so the dialog "start-up" time is 2X times faster now. This might be very substantial for large images and large number of timepoints.

Anatomy constrained IDIF extraction function: Continuing testing\debugging.

Will output vessel ROI resembling a tube of the
specified diameter.  User has to specify "dominant direction" for the vessel.
Otherwise parameters are similar to the old IDIF variant.

Performed initial evaluation of BiCal algorithm on Greg Chang's 7T hip dataset.

Non-uniformity (measured by 48 manually placed seeds) is reduced from the original NU=0.397, down to NU=0.127.

original with seeds,  NU=0.397

BiCal-corrected, NU = 0.127

FireVoxel Build 128I is released.

Provided an additional  Perfusion-IF adjustment variant when both Peak and Tail of the curves are used for matching.  Additionally provided User an option to enter the Peak scaling constant.

FireVoxel Build 128H is released.

Verified that present Sokoloff model is working with new "Adjusted Perfusion-derived IDIF".
Note (!), in limited experiments, Constant-extended IDIF worked much better than the truncated IDIF.

Implemented a stand-alone function for Perfusion-IF  adjustment using PET-IF.  This approach allows to reuse existing Sokoloff model and NOT to introduce custom Sokoloff model, resulting in simplicity. User has an option either to Truncate  adjusted IF, or extend by the last constant.

User Saves adjusted IDIF using "Save" button, then loads it as a regular input function into Sokoloff.

Finalizing the Dialog "Specify two file names".  This is required to Perfusion-derive IF adjustment to PET

Sokoloff model - Revisited "Delay" fitting parameter.  Ensured that when  "Max Delay" option = 0 before model calculation,  the resulting Delay parameter remains 0 (i.e. optimization is done by K1,k2,k3 only).

Investigated "arrival time" difference issue between Data TAC and Model Curve. This seem to work well now, at least for the PET-derived IDIF.

Implementing the "Sokoloff Model with the perfusion-derived Input function"

Verified quality of registration of GRASP-4D to PET4D.  First timepoint of GRASP is cropped and the regular   Applications>PET>Register to Anatomy function is used.  Result is below in several projections.  PET (in RED) is overlayed on top of  GRASP (blue).

Notice substantial (~10 degree) rotation angle between  GRASP and PET.

When saving TAC to file or Clipboard, and appropriate Header is placed before the 2-column data. In the following format    "Dynamic Component (Dynamic Units)  - TAB - value"  so it is suitable for an easy incorporation to Excel.

Enabled saving the "Fitted Curve" from the RoiStats4D dialog.  When user chooses "Save (to file)" or "Copy (to clipboard),  Dialog choice appears that allows to select either "Active ROI" or "Fitted" curve.

FireVoxel Build 128F is released.

1. Implemented initial variant of PET 4D correcction. It is located under MainMenu>Applications>PET>Register 4D (Eliminate motion)
2. In ViewTAC, and RoiStat4D dialog, when the curve is drawn the current Dynamic Index node is marked with the alternative color.
3. Correct  "Edge Constrained Smoothing" function so the "Fill Void Voxels"  option works correctly. Removed redundant code.
4. Corrected the defect in the Progress indicator "with User interruption" function.  This was causing problems that manifested as DICOM loading problems.
5. Corrected the PET-DICOM loading failure that appeared in Build 128D.
6. Fixed the error with PET frame timing due to a simple typo error.
 

Corrected the defect in the Progress indicator "with User interruption" function.  This was causing problems that manifested as DICOM loading problems.

Fixed the error with PET frame timing due to a simple typo error.

Corrected the PET-DICOM loading failure that appeared in Build 128D.

Conducting a short evaluation for the next generation of BiCal non-uniformity conversion tool.  Focus is on using the Gradients instead of Edges for delineating regions of homogeneous tissue.

Correct  "Edge Constrained Smoothing" function so the "Fill Void Voxels"  option works correctly. Removed redundant code.

Prototyping a new IDIF function variant, that would explicitly incorporate an explicit anatomy constrained:  namely a tube with the width of the vessel.  User specifies one of the {X,Y,Z} prevalent
directions.

In ViewTAC, and RoiStat4D dialog, when the curve is drawn the current Dynamic Index node is marked with the alternative color.

Implementing and initial variant for PET  4D motion compensation.  This is based on Dr. DeLeon comment during IDIF meeting.  Additionally a substantial rotation is observed (~2 degrees) betweeen MRI and some of the PET timepoints.
Standard 4D registration is used with some improvements to determine PET forground mask. Main challenge here is the speed of the registration due to the high PET timepoint count.

Investigating the reslicing problem after the registration.

Correcting the IDIF function,  for Axial-SingleSlice variant.  It should behave correctly in {NoSeed,SingleSeed,MultiSeed} modes.

FireVoxel 128D is released with the   4DPET-MRI scenario fixes.

4DPET-MRI registration:   Corrected the workflow so user could choose the "Best" or maximum resolution evaluated individually at each axis.  Registration result is good.  Importantly, notice a non-trivial rotation angle between MRI and PET.  On this screenshot they are registered, but observe the MRI slanted margins, indicating ~2 degrees relative rotation as determined by the registration.

Helping to process the MRI+PET case obtained from Dr. Wahle.   MRI is in Axial, which is different  from the documentation.

Updating the IDIF function for a case when no MACRO-seed is present at all and instead user chooses simply the slice on the Axial projection.

Play 4D function:

• Rewind if we are on the last frame
• Use the default the interval to the last one used
• Indicate the use of real intervals

Investigating a substantial memory residual remaining after the PET-to-MRI registration  ABT subtest.

Updating the Automatic Build Test   for 4D-PET and MRI co-registration.

Dialogs   {AutoFocus3D,AutoFocus4D} :  removed "URAL Interpolation" parameter with the purpose of simplifying registration User Interface.   URAL Interpolation = true, in all registrations.

Documenting the changes in the PET workflow after the change to the Axial projection.  Updating the manual.

Found solution for the registration of the Femur\bone ROIs. This is for the same patient, longitudal study.

Updating and restructuring the registration workflow to principal Axial-projection and accommodate new requirement to either reconstruct to Anatomy or PET resolution.

FireVoxel Build 128B is released.

Made Parametric Calculation call smarter - in case there is a single 4D layer is present, it is selected automatically and User does not have to make it Active.

Major code refresh for:
Dynamic Processing dialog box
Dynamic parametric map calculation - UI Application level
All models in Dynamic Processing DLL are revisited for
parameter consistency.

Parametric modelling dialog layout is rearranged to accommodate longer labels automatically generated for Input Functions.

RoiStats4D dialog:  when TAC for the ROI is obtained, its label is automatically formed consisting of the Roi Name + ROI size in mm3.  This allows user to avoid manual typing in when importing the Input Function inside the Parametric Modelling dialog.

Dialog Roi Stats4D:  Added the "Show Median"  checkbox (as apposed to "Show Average") .  Roi TAC is shown either in Median or Average mode. Same choice for Saving and copying it to the Clipboard.

FireVoxel Build 128A is released.

RoiStats4D dialog:  when "Show All" checkbox is ON,  only Enabled layers will display the TACs.

Improved behavior in RoiStats4D function.  When F4 button is pressed and there are both 3D and 4D layers are present, 4D layer will always be chosen, even if 3D is Active.  This eliminates annoying messages "4D layer is required".

UI change:
Function key F3 is reassigned to be   a "Roi Stats 3D" function
Function key F4 remains a "Roi Stats 4D" function = SHOW TAC
Former key F3 is now F2 for the "Copy ROI info to clipboard" function.

The reason for the change is that often a dynamic image is overlayed
on top of static 3D, so getting TACs often pops up the "4D layer required"
which requires user to bring up the Layer Control box, change active layer
and so on.

Completely re-engineered the 1st Model parameters to make their meaning more clear.

Model Name   = "Signal measurements within time interval";
{ "Signal Spread","Mean Signal","Max signal","Signal StdDev","Sum of absolute signal changes",
"Turbulence","Max Turbulence","Turbulence Count" }

Integrated the "Process Interruption Feature" across FireVoxel.  For any process that displays the progress bar, if user press ESC button, function gracefully exits.  94 locations were modified, only few were tested but expected all to work correctly.

Substantial redesign of the Play4D function:  Movie plays in all available projections simultaneously,
dynamic coordinates, such as b-value, are displayed and movie sequence is in this active dynamic dimension order.

Additional feature,  movie is played in all available views of the selected document
(f.e. all orthogonal projections)

Integrating general UI functionality so that any process that outputs the progress bar may be interrupted by User pressing ESC button....

Fixing a problem with  DlgSpecifyDouble dialog box...

FireVoxel build 127B is released.

Play 4D movie function:  completely re-engineered, removed the defect.  Added a progress bar to the play function.  Additionally user can specify the interframe delay in seconds (real).

Get IDIF function User Interface:  provide a more intuitive user interface especially in the presence of multiple ROI layers, so that no "Ambiguous layer configuration..." message does not show up

After integrating time delay parameter, a new fitting result.

Sokoloff model:   Integrating the "Time Delay" fitting parameter. At the very least, this time delay parameter should be in [0,FrameTimeDelta] (=[0,15] sec) as this is the temporal resolution of TAC.

Updating the Sokoloff model.  During the demo to Fernando, observed that in "naive convolution" calculation upsampling time to 1 sec makes a big positive precision difference.  But this is computationally expensive and additional Upsampling Interval parameter will add to parameter list.
So instead attempting to upsample only the IRF ( Impulse Response Function) and integrate fast convolution technique from:

Fast and accurate voxel-by-voxel perfusion imaging using convolution models.  Artem Mikheev, Henry Rusinek.  Image Analysis - Parametric Mapping Session at the ISMRM 2008 Totonto, CANADA.

Revisiting Volume Smoothing function and ensuring it works correctly on all of combinations of:
{Real,Integer}x{3D,4D}x{ROI,no ROI}...

Fixed the problem with MainMenu>ROI>Threshold To ROI function.  Corresponding Build 127A is released.

Implementing the Sokoloff model with simple fitting by gridding+Amoeba....

FireVoxel Build 127 is released.

• Developed  the PET Workflow Quick Start manual.
• Produced the initial result for the Image Derived Input Function. 
• Implemented Vt (Logan) plot parametric model based on the newly available technology for the Image Derived Input Function from Carotid Artery.
• Corrected the defects that came up during the presentation to Fernando.  These two bugs are intermittent and are hard to reproduce.
• Implementing a new version of the "Blood Vessel Finder" dialog based on the initial discussions.
• Finalized 2nd generation of the IDIF (Image Derived Input Function) dialog. Principal addition is the introduction of L2-based measure for checking TAC similarity.  However, L2-smoothing was introduced in a way so blurring of the TAC is avoided.
• Extending the IDIF functionality so several seeds can be specified covering branches of the Carotid Artery to create larger ROI and thus more reliable Input Function. Since the IDIF function is very fast this is done simply by calling procedure several time and OR-ing corresponding ROIs to create the final one.
• Documented the latest version of the semi-automatic IDIF tool.
• Fixed the "Missing time information in save .IM file"  reported by Dr. Rusinek.  This was due to the time written in "absolute value" and using the scientific notation some important lower digits were truncated.  Switched to the regular "double float" format by using %lf option in fprintf().
• Fixed parametric map-related defect:  when  RoiStat3D  dialog display statistics, the VOID voxels are included into the calculation.  They should be excluded.
• Simplified the "Real Volume to Integer conversion" menu item to perform conventional rounding with the truncation to the specified bit length.'

Simplified the "Real Volume to Integer conversion" menu item to perform conventional rounding with the truncation to the specified bit length.

Fixed parametric map-related defect:  when  RoiStat3D  dialog display statistics, the VOID voxels are included into the calculation.  They should be excluded.

Fixed the "Missing time information in save .IM file"  reported by Dr. Rusinek.  This was due to the time written in "absolute value" and using the scientific notation some important lower digits were truncated.  Switched to the regular "double float" format by using %lf option in fprintf().

Documented the latest version of the semi-automatic IDIF tool.

Extending the IDIF functionality so several seeds can be specified covering branches of the Carotid Artery to create larger ROI and thus more reliable Input Function. Since the IDIF function is very fast this is done simply by calling procedure several time and OR-ing corresponding ROIs to create the final one.

Verified that the Macro Seed for the IDIF may be specified on any of the orthogonal projections.`It makes it possible to specify the Macro Seed on the Axial projection where Carotid artery can be found easily.

Finalized 2nd generation of the IDIF (Image Derived Input Function) dialog. Principal addition is the introduction of L2-based measure for checking TAC similarity.  However, L2-smoothing was introduced in a way so blurring of the TAC is avoided.

Implementing a new version of the "Blood Vessel Finder" dialog based on the initial discussions.

Fixed the registration mishap during the presentation.  After PET->MR registration, the time automatically advances to the first timepoint where PET signal is non-zero.

Correcting the defects that came up during the presentation to Fernando.  These two bugs are intermittent and are hard to reproduce.

Implemented Vt (Logan) plot parametric model based on the newly available technology for the Image Derived Input Function from Carotid Artery.

Implementing Vt (Logan Plot) suitable for FDG based on the latest IDIF availability.  Model Interface is almost identical to the PMOD.

Presently implementing support functions for manipulation Input Functions within the Dynamic Processing module.

Produced the initial result for the Image Derived Input Function.  This is developed for the PET FDG priority at the moment.  However, function is just a very general "Input Function Vessel Detector", so can be used in the DCE studies too.

Briefly, after PET is registered to MRI, workflow is as follows:

• User specified a very approximate rectangular region containing carotid artery.
• User specify a single "Vessel Homogenity" parameter as a percentage (f.e. 70%)
• Automatic process follows, the IDIF   TAC dialog pops-up for the inspection
• Dynamic Framework Input Function is populated automatically so the user can proceed immediately to kinetic models.

Additionally, FireVoxel provides a simple and fast tool helping User to find an approximate location of Carotid artery.

Have an algorithm outline for the PET FDG    Image derived Input Function.  Started UI implementation...

Implementing automatic OR possibly semi-automatic procedure for Image Derived Input Function (IDIF) extraction from FDG PET dynamic volume.

Continue work on the PET Workflow Quick Start manual....

Investigating the core functionality of DCMTK library for converting their internal DICOM header structure to the library-independent tree structure of the FireVoxel.

FireVoxel Build 126A is released.

Corrected the ADC  diffusion parametric model so that the fitting can be done even when only 2 timepoints are present.

Creating the "PET-workflow QuickStart manual"....

Official Build 126 is released to testing.

2.  Removed the "by-default" calculation of Source and Target noise in AutoFocus 3D\4D.

3.  Changed the linkage of the Dynamic Frame work DLL, so all the supporting DLLs can be used directly without redundant duplication.

4. Moved all Amoeba code into the PWR dll so it can be accessed by the Dynamic DLL.

5. Removed the IVIM with background model.

6. When dialogs RoiStat3D and RoiStat4D are acivated, the "ROI is empty" error message is displayed,  show the name of the ROI layer.

7.  Register sing Landmarks dialog:  fixed several problems in specifying the name of the Transformation  .vtf file.

8. "View TAC" dialog box:  added the "Voxel Radius" parameter so the TAC could be averaged over the cubic vicinity of the cursor.  This results in seeing smoother TACs. Parallelized to work smoothly over the volumes with the hight # of timepoints.

9.  "Landmark registration with autofocus" is changed to "Landmark registration + Voxel similarity", execution crash was fixed.

10. Fixed an intermittent error in the core Registration procedure, when registration image padding was calculated based on the URAL radius, while that radius was undefined due to the different registration measure used (i.e. non-URAL, f.e. MI etc)

11. Defect: crash in T2\T2* mapping model for the 4D abdominal volume provided by Henry. Fixed: the problem was in incorrect handling of timing data, when the Dynamic Component is different from TIME (ECHO in this case).

12. Fixed defect:   4D registration would not initialize for 4D Real-valued volumes such as PET.  Presently, 4D registration with Mutual Info was tested on 4D PET volume.

13. Fixed the  3D Edge Detector function to work properly on the Real-value volumes such as PET.

14. Fixed the  3D Texture Gradient function to work properly on the Real-value volumes such as PET.

15.  Problem with Alpha-combining the White-color ROI is due to that the White color 24-bit value of 0xffffff is also used as a transparency voxel code..

16. Added a warning message to 3D and 4D registration dialog boxes.  When the user have chosen the URAL-UNI registration measure, but the Sorce\Target Noise were not specified, the warning is displayed when user presses OK button.

17. Implemented averaging function for Signal Intensity and Real-valued volumes.User specifies the Time Index interval for averaging. Resulting REAL valued volume is overlaid on top of the original 4D.

18. Implemented the Mead-Nedler (simplex\Amoeba) optimization algorithm MDS (multi-direction search) variant.  This is inherently parallel algorithm, presently verified working in the serial workflow.

Presently: inserting parallel instructions to fully utilize MDS parallelism.

19. Enabling registration of REAL volumes using Mutual Information measure.  Presently the code is only working for 16-bit volumes (that was used to show PET->MPRAGE prototype).  Solution is to convert to 16-bit correctly while binning the voxel values for the MI.  This is also strongly related to a proper binning for REAL volumes, so it is addressed at the same time along with the corresponding binning interface  in the registration dialogs.

20.  In Registration Finetune, both 3D and 4D, adding a "Multipass" option corresponding to initiating Amoeba algorithm several times.  This optionally achieves higher registration scores at the expense of the execution speed. 

21. Creating a fully integrated workflow of 4D PET registration to MRI, so that user does not have to manually crop and change orientation of PET prior to registration.

22. Fixed defect:  when any type volume is displayed, if user presses ViewFilter for this volume, there is a fairly long wait and the "Compute Histogram" message is displayed.  This was fixed by removing Histogram recalculation and instead using compressed block header access without decompressing the blocks themselvves to find maximal voxel value of the volume.

23.  Corrected the logic of automatically finding an optimal window\center for displaying the image for all kinds of volumes (i.e. Real and Integer). Problem is in 4D cases, only the 1st timepoint is evaluated to reduce the processing time. But first or any other timepoint might contain almost no signals thus leading to a non-sense settings and strangely displayed volume.

24.  Fast loading of the native *.FVX file:  98% of time is spent    DCMTK::FindTagName function.  Result:   "Native" loading of the original DICOM 5.6GB dataset is now 0.7 sec.

25. Highly parallelized Volume cropping function (UI-level), so it runs much faster now.

26. Achieved final registration of PET to MPRAGE.   It is part of the ntegrated registration workflow that includes automatic cropping and orientation correction (from coronal to sagittal).

27. FilmView display:  for large images it is quite slow, with 4.8 sec to display all slices of 344x344x170 volume.  Fully parallelized with the x3.5 speed-up (down to 1.37 sec)

28. Eliminated the need for the user to specify the "anchor timepoint" during the PET to Anatomy registration.  Timepoint of Maximum average singnal is selected and the registration is performed to that timepoint to determine the required transformation for all PET timepoints.

29.  Implementing MRTM0, MRTM, MRTM2 reference model within the FireVoxel Dynamic Processing framework.

30. Fixed  the DICOM-ROI   save and edit problem reported by Alexandra Hotca.

31. Fixed several problems when trying to load a single DICOM slice directly from multi-slice DICOM tree.

32. Fixed defect: When ROI is saved to DICOM it is incorrectly displayed in Oped DICOM dialog Preview panel.

33. Fixed an error writing incorrect datatype in ANALYZE 7.5 format (for 16-bit volume)

34. Added the progress indicator to the FireVoxel document load. This is very helpful when loading very large volumes (such as PET)

35. When dialogs RoiStat3D and RoiStat4D are acivated, the "ROI is empty" error message is displayed,  show the name of the ROI layer.

36. In Dialog ROI  Stats 4D:  added a function to copy TAC to a clipboard in format so it could be easily pasted to Excel without saving to a file.  Also, changed the formatting of  TAC file to include \t to import easily to Excel.

Fully cleared and corrected the test logic for ABT on FireVoxel Build 126.

Added a warning message to 3D and 4D registration dialog boxes.  When the user have chosen the URAL-UNI registration measure, but the Sorce\Target Noise were not specified, the warning is displayed when user presses OK button.

Fixed the Phillips diffusion loading problem. The standard b-value DICOM Tag is used,  but different from GE and SIEMENS, the b-value was encoded as double floating point.

Investigating DICOM Rescale\Intercept problem with the Philips diffusion volume.