Registered 4D CorDiff volume to the last timepoint (echo time) of GreCor volume. Last timepoint was chosen due to the highest contrast between the kidney and surrounding tissues.

Target kidney ROI first need to be constructed on the target (GreCor) either manually or automatically (manual in this example).  No ROI required on source (moving image).  However, registration relied on the fact that the volumes were acquired as part of the same exam so DICOM tags can be used for the initial alignment which is then finetuned by registration procedure.

Rigid registration was used in this example.  However, the volumes have very non-isotropic voxels

(1.5,1.5,7.5) mm, so the assumption of rigidity is very questionable and elastic deformation  may be used instead.

 

 

Optionally, the Target volume was made isotropic (1.5)mm^3.  This way the amount of information lost during the final reslicing is minimized.

Build 345 is released.

 

 1. Changed the automatic baseline calculation in the general Signal-to-Concentration conversion function.

2. Reduced internal MAX number of Input Functions to 4 (from 5). This was causing problems and crashes with displaying them, since the Dynamic Experiment dialog has only 4 slots.

3. Implemented the "Cardiac Output Measurement" tool and corresponding dialog.

 

 

 

 

3. Concentration conversion dialog:  implemented the 6--entry long relaxivity table using three dropdown combo boxes.

4. When saving to FVX file format, removed the DICOM tag PatientID from the list of PHI.

5.  Extended DICOM read to include the fix of files with deliimation errors. This resolves the load of the problematic PET file.

Build 344A is released.

 1. Implemented DICOM loader extension for files when the logical 3D volumes are intermingled along the time axis.

2. Added ABT subtest for DICOM "Intermingled-load".

 Prototype workflow for automatic whole kidney and compartamental segmentation on GRE data.

1.  Atlas of the kidney was constructed manually from the Patient (id  PP506).  Last TE timepoint (=30.53 ms) was choosen where the contrast between kidney and surrounding tissue is the maximum

2.  Another patient ( RH.41.L)  GRE dataset was chosen for segmentation.  At the moment we ask User to enclose the kidney with the bounding box in the mid-slice. Again the last TE timepoint (39.36 ms) was chosen to maximize the contrast between kidney and surroundings.

 

 

3. Internally full 3D bounding box is constructed which encloses the kidney.

 

4. We activate Large Deformation registration of the Atlas into the rough bounding box of the kidney.

 

 

 

5. After registration runs we get the Whole kidney mask and {Cortex,Medulla} masks over the 2nd patient. Note: the target volume was resliced to isotropic 2.08mm^3  to minimize data loss during the reslicing (since the Z-resolution is very coarse 5mm).

 

 

6.  Same result as above but displayed without Cortex mask.

7. Future improvements:  have better higher resolution Atlas, perhaps even from different protocol.

Have several atlases, match to all and select the best.

Alternatively, only the Whole kidney mask can be registered and then Whole mask can be separated into Cortex and Medulla.  Histogram thresholding is typically not working well for that purpose, so more locally adaptive operator should be used.

8 Below is one such result.  Whole kidney mask was taken from the result above, but then we used Detect Dark Ridges (default parms) to split the Medulla and the remainder is Cortex.

 Kidney registration from pCASL data to GRE data.  Last TE point of GRE was selected to draw ROI due to a better contrast with surrounding tissues. Then pCASL was registered using initial DICOM tag alignment with further Rigid registration using Mutual Info.

Each kidney has to be done separately at the moment, but a single click workflow for both kidneys is possible.

Three screenshot below demonstrate reegistration results:

a) GRE  ROI overlaid on top of the registed pCASL volume.

 

b) pCASL (in green) overlaid transparently over GRE (red)

c) Separately, GRE was turned into isotropic  2.08 mm^3 to minimize pCASL information loss during reslicing, then same registration was performed.

Build 344 is released.

  1. FLEXR3D registration : fixed defect in final layer construction was causing a crash.

2. Fixed the "invalid units" defect when output ADC model mm^2/sec. Now displayed properly.

3. Implemented functions for swapping Transparent (VOID) value <-> User Specified value.

4. Fixed defect: Volume Redraw cache  was relying on a simplistic CheckSum algorithm which sometimes return incorrectly TRUE causing the document Window not to redraw after the operation. Improved the CheckSum function, so old defects are properly redrawn.

5. Model #16  "T2 and T2* mapping":  changed name, some unit options etc.

6. Volume>Crop Current Slice : upgraded function to crop all existing slices. Reused the common code VolCrop function.

 7.   Chest Area  Muscle\FAT measurement: fixed defect "instead of MAT, 343A repeats the fat volume."

 8. Fixed defect when adding new layer (such as ROI) was producing incorrect Vz resolution for the new Layer. This was causing frequent "Resolution mismatch" messages.

9. Fixed the Colormap collapse problem when Color Window Width is set to 1.

 

0. Manually constructed ROIs on Cor-Diff and Cor-GRE cases. 

Cor-GRE case was not Motion-Corrected since it was a breath-hold, but additional Motion-Correction is possible.

Each kidney should be processed separately in this workflow.

 

 1. Performed R2 fitting on kidney from Cor-GRE case

 

2. Performed motion correction of Cor-Diff case and produced and ADC map.

(Motion correction    Workflow>Renal Multislice>Motion Correction (In-Slice) (MI).

 

 

 

 3. Performed registration of Cor-Diff case to  Cor-GRE cases (using FLEXR3D 2mm)

Base Cor-GRE is shown in Green, then overlaid with Cor-Diff (in Red) with 50% transparency to demonstrate registration match.

 Build 343A is released.

1. Corrected slice # to be 1-based in report generation for "Segment Chest Area Muscle" function.

2. Implemented File>Minimize DICOM Headers function to remove extra info from DICOM and sometimes greatly reduce the resulting FVX file size.