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.