FireVoxel Build 394 is released.

1. Lateral Ventricle segmentation : Updated end expanded parameter set, updated the dialog box.

2.  WML segmentation from (FLAIR+MPRAGE):  updated the algorithm to deal with the hollow lesions (GM oversegmentation).  Updated the dialog box.

3. Fixed crash problem with the FLOAT32 NIFTI image.

4. Fixed the defect "Change Resolution New Dimension" support function

5. Implemented new function :  MainMenu>Transform>Change resolution

6. Implemented a new version of FVX file format (#14).  It compresses all the internal DICOM headers together.

Build 393 is released.

 1.  ROI Inflate function (using DrawVic) - parallelized for x4 speed up.

2.  Fixed a "non-initialized memory" defect. When .IM file was loaded the ImagePosition was not initialized, so when it was not 0 - it lead to the resolution calculation failure.

3.  DICOM image crash : fixed situation when sequence element is present but does not contain a value.

4. Implemented the new BiModal Histogram Split dialog (allows both Peak Ratio and optional Mass Ratio)

5. Implemented new Histogram segmentation methods {BiGauss,BiLaplace} ratio constrained including optional mask ratio.

6. New version of WML segmentation tool (from FLAIR+MPRAGE) with the updated GM segmentation based on Mass ratio.

7. Volume registration using DICOM tags:  fixed the defect so that the resulting layers have ViewFilter and the Mark identical to the source layers.

Build 392B is released.

1. MainMenu>Measurement: MutualInfo  : works now on 4D volumes, or a combination of 3D and 4D volumes.

Build 392A is released.

 1. Fixed opening of the Ultrasound DICOM file. This was due to the presence of the VR_AT attribute.

2.  Individual measurement of the Mutual Info (under Measure) menu:  removed multiplication by (-1) which is used in registration task context.

3. Measurement MI: Fixed improper memory free that was causing a later crash because images were deallocated.

4: Dynamic Analysis: Calculate Cross4D Mutual Info items:  moved to under the Measurement Menu.  Removed the (-1) multiplication.

Build 392 is released.

 1. Fixed: Background voxels in NII are assigned value which is Not A Number (NAN = i.e. sequence of bytesthat have no meaning as a floating point number). 

So FireVoxels loads those voxels as VOID.  User has an option to save it back to NII, than FVX shows the dialog "Replace VOID voxels with X".

2. Histogram segmentation:  removed PVV and Zigalga methods from the User interface. They are still used in legacy workflows.

3. Integrated the Gaussian Mixture Models c++ code.  Exposed the GMM model as the HIstogram Segmentation.

4. Removed the PVV and ZIGALGA methods from User Interface.

5. Fixed the crash: Loading a {ANALYZE,IM} file, VROI, Crop.  This was due to the missing Dynamic Coordinates.

6.  AutoFocus4D dialog box. Performed adjustments, removed the Ensemble algorithm option and corresponding fields.

7. Layer Control dialog: "Remove layers" operation: added a check when all layers are unmarked to prevent crash.

8.  Transform>Rotate Orthogonal  :  now transforms all the layers of the Entity.

9.  Transform>Rotate Orthogonal  :  updates the orientation of the new volume correctly..

9. VROI on multilayer entity:  automatically selects the layer with MaxT for use in VROI.

10. Enclose connected component by the VROI now automatically generates the VROI name.

 1. Volume ROI Bit Operations: fixed the crash when non-ROI volume is supplied. Displays an appropriate diagnostics.

2. Updated version of the WML segmentation algorith: added 2 heuristics:

a) sulci of certain depth are excluded

b) narrow isolated channels inside the brain are treated as sulci and are excluded.

3.  Implemented new GUI function : ROI>Morhphology>Extract Holes 3D

4. Corrected a "Lock out" defect in EdgeWave: when the ROI layer is the source operand and the "Average over Seed mode" is default in the parameters, the EW dialog would not appear and inform "invalid operand for this operation".

5. Fixed UI problem:   Brain Segmentation UI used the same parameter variable as the general EdgeWave item. This was causing problems in some complex workflows.

6. Implemented  new UI functions:

Common task, having volume in native projection X, reslice it to a new document in 

one of the major projections {AXIAL,SAGITTAL,CORONAL}

7.

In SetProjection dialog box added 3 buttons to Rotate to major projections  (depending on the UserOptions  RADIOLOGICAL\NEUROLOGICAL )

8. 

Added a function to make current projection -> Native.

9. Implemented "Lateral Ventricle Segmentation" including the respective dialog box.

10. Fixed defect: All Rotations under Transform menu: the Alpha of new layers = Alpha of the original layers now.

11. Moved WML functionality to under the Workflows>Brain MR menu. Kept a single function since it works for all native projections.

12. Added the built-in N3 to WML FLAIR workflow.

13. Developed a stand-alone dialog for WML FLAIR segmentation.

FireVoxel Build 390 is released.

1. Dialog VolumeInfo : Implemented sorting of the DICOM Info by columns {Tag,Name}

2.  Dialogs VolInfo,OpenDicom : added the "Sequence>" prefix for the Sequence descendants.

3. All dialog boxes in FireVoxel:  updated capitalization according to MS GUI guidelines.

Build 389 is released.

 1. VolumeINFO dialog box:  The multi-column info Panel is available for full content retrieval in Notepad through the CopyInfo function.

2. Implemented the Sorting of the DICOM Info {Full,Quick} in the Dicom Open dialog box.

User can press either on Tag or Name header button and it will be sorted.

 FireVoxel Build 388 is released.

1. Open DICOM dialog box.  The info Panel is available for full content retrieval in Notepad through the CopyInfo function.

 1. Dynamic Model 3: Modified names of the output parameters to match the UI timing convention.

2. Major update to NIFTI  Import\Export to fully support the IMAGE_POSITION_PATIENT.

3. If NIFTI Load: fixed the loading of invalid NIFTI files so there is no unlimited loop.

4. Support loading of the incomplete DICOM files with critical tags missing and allow ROI drawing over it.

5. Transform: Orthogonal Rotation: resulting volume is always in "Native" projection now.

Build 386B is released.

1. Fixed defect:  "a tricky DICOM file size 256x256 but it contains an "Unknown" sequence which contains the Columns*Rows = 128x128.Few Builds ago we became more diligent about sequences (remember Louisa's bolus\contrast subsequences). So combined with that file, it makes FVX confused."

2.  FIXED: crash:   while trying to transform 4D volume with SectorRotate\VectorTranslate function. This particular function requires a separate Affine matx for each timepoint. But I was only providing a single matrix to the API.

3. FIXED issue: "When polyline\spline is drawn on non-native projection the FVX file does not remember that projection for polyline\spline object is now shown on the reload. FVX file format was modified for polyline objects (of course all old files will be supported)

Build 386A is released.

 1. Main Menu>Measure>Mutual Info over optional ROI:  now supports 4D volumes.

2. Updated the breast BPE tool report so formatting is suitable for Excel.

 Build 386 is released.

1. Implemented Workflow>Breast BPE maps>Motion correction.  Based on FLEXR a call optimized for motion correction in 2D+t volumes.

2. Implemented BPE Map generation and report.

Build 385B is released

 1. 4D-ROI Volumetric Measurement dialog box: fixed "Copy Curves" functionality to include the Time info and to open the Notepad.exe.

2.  Elongated object measurements:

a) Start-to-End distance in mm reported.

b) 4th column: for each point of centerline a sum of distance to Start and End.

3. Implemented UI function:   >Measure>Mutual Information between 2 layers

4. Curve analysis:  implemented a function to determine "Periodicity" of the curve. Integrated withing the lung workflow.

Build 385A is released.

 1. Remove the Test>ROI Longest Axis Centerline function from UI

2.  Workflow>Pancreas>Longest Axis:  text report now includes the name of the original document.

3. Lung Spirometry FEV1 : modified algorithm for noisy curve, so no negative values are allowed.

4. 2D Lung spitometry: modified curve analysis process so the peaks and bottoms are identical for L&R curves.

5.  Added ABT subtest for the FLEXR- MC Segmentation procedure.

Build 385 is released.

 1. Implemented prototype of Lung diaphragm movement detection and display.

2. Fixed the defect: Crop current timepoint in 4D volume was sometimes causing a crash.

3. Developed new segmentation algorithm for 4D Volume segmentation based on FLEXR-MC.  User draws organ ROI on the first timepoint and the procedure segments\registers that ROI on all remaining timepoints.

4. Fixed defects inside the FLEXR-2D algorithm.

5.Processed 8 patient cases for lung exam 2D+t, developed the Measurement reporting to characterize the lungs.

6. Defect fixed:  In ROI stats4D dialog when saving the TAC or copy clipboard, the signal value output was always positive (abs).

7. Defect fixed: when 4D volumes (without ROI) generates a parametric model in "As a single curve" mode, Report is pressed and the crash occured.

8.  Fixed situation: when NIFTI image file contained NAN FLOAT32 (not-a-number).  Such voxels are assigned 0 value instead so the loading could proceed.

 FireVoxel Build 384A is released.

1. Implemented new workflow item :

 MainMenu>Workflow>Pancreas>Measurement along Central Axis

2. For pancreas, the start of the axis is assigned to the End with the left-most coordinate. Provided an API for custom Axis Start logic.

3.  Axis measurement tool outputs text report that contains both the name of main layer volume and ROI.

Build 384 is released.

 1. Developed procedure to detect local Min/Max in Spirometry volumetric curve.

Note filled circles here designate the Peaks and Trenches of the volumetric curve.

2. Developed procedure to fold the spirometry lung volume curves into a single average cycle. Provided a specialized dialog for it.  Dialog allows to switch between "Full curve" view and the "Cycle-only" view.

3. Added options to Lund Function  dialog to display {Full Curve, Cycle, Inspiration, Expiration} curves.

4. Fixed the defect when loading the FLOAT32 .NII file resulted in the volume be uniformly = 0.

5. Updated internal NiftiToDicomOrientation function.

6. Developed a Free-knot Spline approximation for the Function graphs. Was applied to the Lung curves (both Full and Cycle).

7. Modified the Binary Load for the NIFTI   FLOAT32/FLOAT64 files to detect if the file is actually an ROI.

FireVoxel Build 383B is released.

 1.  Fixed the crash when cropping a single slice from a 2-layer document and there is a resolution mismatch (was caused by a negative SPACING_BETWEEN_SLICES, with negative being legal under DICOM).

FireVoxel Build 383A is released.

 1. Corrected the mouse lag issue: specifically in Raster paintbrush, but also this improved spline function and VROI definition.

2. Raster paintbrush: corrected dialog box so the Radius is measured in (vox)

Build 383 is released.

 1. Fixed the SAVE\RELOAD defect when saving FVX document including the polyline OR spline.

2.  Added functionality to SAVE to DICOM   volumes of type FLOAT64.

3. Implemented improvements to the "Fix DICOM Tags" tool.

FireVoxel Build 382 is released. 

1. Volume Information dialog:  DICOM header is now displayed with Nesting up-to level 1 (so some sequences are shown as part of the Dicom Tree)

2. RoiStats 3D dialog:  replaced static text elements with the Edit Control (read-only,Multiline,Transparent) so that User can select and copy any text inside the dialog box.

3. Implemented a custom "DICOM Tag fix" function.

Build 381 is released.

 1. Fixed important crash defect in IsVoidVoxPresent function.

2. Modified the optional REAL loseless compression scheme getting x2-x4 compression on real PET images.

3. Reimplemented Huffman compression API for 1-byte value buffers.

4. Updated internal lossless compression for REAL images:

PET image with 60 timepoints, 400 MB of data is LOSSLESSLY

compressed down to about 50MB (x8 compression). This compression is optional (managed through UI Options dialog), only slightly slower. Also would reduce the size of the FVX file if saved.

5. Code optimization for internal compression of ROIs, somewhat higher speed possibly will be noticeable while drawing on ROIs on slower computers.

6. Pancreas axis segmentation: added the centerline length info to the output and the Clipboard Output.

 FireVoxel 380A is released.

1. Pancreas ROI segmentation: updated the algorithm to reduce the small starting generations in Wavefront segmentation.

FireVoxel Build 380 is released.

 1.  FVX file load\save: added extra diagnostic into the Polyline object loading.

2. Set Orientation\Position dialog.  Corrected behavior of "Align to Scanner" when the original orientation is undefined.

3. Removed redundant design from the Orientation\Position dialog box.

4. Implemented first prototype of the Pancreas segmentation and measurement tool.

Build 379 is released.

 1. Volume>Change voxel values   menu:  changed the "Transparent" item names to "VOID" to reflect exact meaning.

2.  When volume is saved to {NIFTI,MIDAS.ANALYZE}, the volume is tested for having VOID voxels and if so the User is asked for the new value to replace void voxels.

3. All AutoFocus registration function:  fixed defect when the opened Layer Control dialog would not correctly update after the registration.

4. AutoFocus 4D registration: Fixed crash defect when no Target ROI is present.

Build 378A is released.

 1. Fixed the defect when loading NIFTI images of FLOAT64 data type.

2.  Replaced the ROI "Inhomogeneity" in various locations by the "Coefficient Of Variation"

 1. Introruced new prototype function :  "Elongated ROI median axis segmentation" that provides slices along the median axis.

2. Implemented FVX file save verification.

3. Nifti: implemented code to support the negative values in INT8, INT16, INT32 (old version was truncated). If negative value is present we represent volume as REAL.

4. Nifti: implemented code to support  SLOPE\Intercept (old version was ignored). If non-trivial slope\intercept are present, then we represent volume as REAL.

Build 377 is released.

 1.  New way of saving IMAGE file:  there is NO *.time option now. Instead user selects the {.IM,.IMG,NIFTI} extension and the .TIME file is created implicitly.   This way there is no need for the second dialog to specify "4D Flavor" (MIDAS,ANALYZE,NIFTI)

2. Fixed defect in loading the VTF file (saving was done as UNICODE, but loading was done is ASCII, so defect was happening).

3. Fixed layer problem in AutoFocus3D registration.

4. VROI file:  changed both Load\Save to UNICODE text file.

Build 376 is released.

 1. Implemented NIFTI4D save as a single file with the supplemental *.TIME file.

2. Fixed defect MainMenu>Measurement>Two Volume RMSD (crashed when Volumes were 4D)

3. Fixed crash when Paintbrush outside the image.

Build 375 is released.

 1. Fixed crash in Registration>Landmark+AutoFocus.

2.  Modified function , provided new UI for the Lung MRI 4D Single Slice processing.

3. Fixed defect:   when creating VROI in multilayer document, the possible Time Interval for the VROI is now defined by the ActiveVolume (before it was MainVolume)

4. 4D registration and Motion Correction function are now displaying the VTF4D file after the execution which could be saved afterwards.

Build 374A.

 1." InterVolume edge constrained smooth" item was moved to under Test menu.

2.  Certain NIFTI files were causing the sporadic message during loading  - removed

Build 374 is released.

 1. NIFTI file load:  fixed defect when the sform_code was improperly handled. Added the diagnostics message.

2.  NIFTI file Save: fixed defect when sform_code default was=0 (but it it invalid).  Now changed to default=2)

3. Enable the load of *.TIME file associated with the NIFTI4D file (either .nii or .nii.gz)

FireVoxel Build 373 is released.

 1.  Volume>Adaptive threhold function :  renamed and moved to ROI>Local Otzu Threshold to ROI,

Code is fully reworked and now works on {INT,REAL} volumes. Dialog box for a single parameter is added.

2.  Volume>Voxel Value Conversion>Flatten Histogram  is renamed Equalize Histogram.  Algorithm is changed to match the classic description of Histogram Equalization algorithm.  Works only for 3D Integer volumes.

3.Volume>Voxel Value Converison: reimplemented the function so it works on all volume types {ROI,INT,REAL}. Added progress indicator.

4.  REDO functionality:  fixed defect so that the ViewFilter is properly restored after REDO.

5. Registration>Landmark registration  : corrected defect when there is mismatch in the number of landmarks the diagnostics was improperly displayed.

6. Changed the definition test for the "empty landmarks". Removed automatic deletion of "emptty landmarks" from Landmark Registration.

Build 372A is released.

 1. Modified Texture Edge Detector dialog : Threhsold units are now properly marked.

2.  Volume Menu:  changed the item from "Multiscale Texture Gradient 4D Aggregate" -> "Multiscale Texture Gradient 4D Max"

3.  Undo\Redo architecture:  corrected the design so not only the pixel data is saved in the UNDOREC but also the corresponding VIEWFILTER settings since the operations usually followed by  the change to the VIEWFILTER (f.e. after smoothing).

4.  Volume Dynamic Smoothing:  fixed defects

      a) Smoothed correctly along the dynamic dimension (before across time only)

      b) Correctly accounted for VOIDVOX presence.

5.  DICOM Folder browsing: removed legacy restrictions on the allowed DICOM extensions. This was redundant, because further checks are done for DICOM header. Now any DICOM extension is allowed.

Build 372 is released.

 1. Volume Edge-constrained smooth : Fixed the "crash" and changed the progress report to individual timepoints.

2.  Volume : Smooth (over Optional ROI):  extended so it works with volumes containing VOIDVOX.  Also unified processing so all the possible kernels are working from the same code.

3. RoiStats4D dialog box initialization : Corrected crash defect

4. Mutiscale Texture Gradient 4D aggregation: restored the functionality based on the common code with MSTG.

5. Volume Menu:  replaced "Texture Gradient" with "Single scale texture gradient".

6. Corrected Voxel weight scheme naming to "Rayleigh" in multiple locations

7. Volume>Voxel Value conversion>Linear Conversion over ROI : enabled UNDO for this operation.

8. In Volume menu ensured that ALL Operations modifying an existing layer are backed by UNDO\REDO mechanism.

Build 371 is released.

 1. Fixed the crash error in (Optimal Window Center Width). Error first appeared in Build 369A.

2.  Implemented a MEMFILE structure.  Similar to the standard constructs in VC++ and Linux but adapted for FireVoxel needs. Allows to write to a FILE (which is MEMFILE and resides in memory).

3.  Upgraded the FVX Save function to work through MEMFILE first and then transferring MEMFILE to a disk file at once.  This should be especially beneficial for the Remote Drives.  Also, it provides a very clear indicator of SAVE progress for large files.

4.  File>DICOM>Dicom Folder Total Pixel size function:  corrected calculation for the files without the compression.

5. Corrected wording in the dialog of the "Specify Signal to Become transparent" function.

6. Fixed the typo in "New value for transparent signal" dialog.

7.  Fixed diagnostic messages for various scenarios under Volume>Volume Type Conversion>ROI to INTEGER.

8. Dynamic Experiment dialog box (Model16) : corrected various naming issues.

9. Fixed various naming issues Model 26 and 50.

10. Corrected various naming issues in Models 24 and 25.

Build 370A is released.

 1. Added more diagnostics to FVX file save function when the target is the Remote drive.

Build 370 is released.

 1. Implemented "NLM denoising dialog".

2. NLM denoising : Enabled 2D processing

3. NLM Denoising: sped up the processing by re-arranging parallel_for construct.

4.  Updated the FVX files Save operation to work smoothly on the Remote drives:

When User selects the Save file name, FVX checks if the specified file resides on the Remote

drive.  If not Remote - operation proceeds exactly as in previous versions.

If Remote (tested on R: drive):

Initially file is saved into FireVoxel temp directory. This is done automatically by FVX and

user has to do nothing.  Once it is saved to TEMP file, there is a single COPY operation

from Temp file to the Remote destination file.  This is optimal for network transfer - all in one

big chunk.  Best of all - it now shows the PROGRESS dialog.  So copying a 100MB file to R:

drive takes 2:45 min.  It shows the standard Windows Copy progress dialog. 

At the end the TEMP file is deleted.  All of it is transparent to the User, i.e. no additional operations

required compared to the local Save.

5.  NLM dialog : Implemented the "Get Noise" button.

6. Updated the Volume menu documentation (v3)

Build 369A is released.

 1. Volume menu : Changed naming "Window Center\Level" -> "Window Center/Width".

2. Volume menu : Changed naming "Optimal for All" -> "Optimal for all slices and dtimepoints".

3. Volume Menu : Window Centerr ... > Optimal for current slice  -> replaced with ->Optimal current ROI". Corresponding code was implemented - now fully functional.

4. Volume>Noise and Air -> renamed Volume>Noise

5.  Model 52 "Gamma Variate fit" :  fixed the output units "sec" issue. Also increased a potential interval for 

beta = [0.1,1000]

Build 369 is released.

1. Implemented a "Harmonized Ta-fit" option for Model #8 (Tofts {Ktrans,Ve,Ta}).

2. Implemented a "Harmonized Ta-fit" option for Model #9 (Tofts {Ktrans,Ve, Va, Ta}).

3. Introduced new optimization type "Simplex (amoeba) harmonized". This allows to remove additional hyperparameter from Model 8,9.  Instead User selects the optimization type from the standrad combo box.

4. PCA-decomposition function : fixed the defect when there is no exit on Dialog box Cancel button.

5. In various UI operations removed legacy limitations on the number of allowed layers (was hardwired to 100, now unlimited).

6. In Projection label letters displayed changed "Head\Foot" ->  "Superior\Inferior".

7. Corrected defect in assigning orientation Letters based on initial Orientation and Projection Rotation. This was a very non-trivial fix due to inadequacy of individual axis matching. Instead 3 axis closest match was employed.

8. Addressed list of issues in the Abdominal Segmentation FAT workflow:

  a) removed cryptic "pz,dz" dialog.

  b) removed the "Missing layer message" : it was due to the original "one step" processing when the ratios were displayed immediately after the segmentation. Now it is done in a separate step.

  c)  Remove redundant "Produce subcutaneous and visceral fat masks (Single Slice)". Operation is presently exactly the same for a single slice or whole volume.

   d) removed the "Convex Hull is empty" message and interruption of processing.

    e) Change the tissue names in the processing menu to {SAT,VAT,MAT}

Build 368A is released.

 1. Fixed the "Missing Block" defect when certain operations would stop with such message. This was due to "legalizing" NULL blocks in recent Builds when they represent a block filled entirely with VOID voxels.

Build 368 is released.

 1. Model 9 (Extended Tofts) :  added a hyperparameter for Minimal IF delay so the negative values could be used.

2. High speed up (x25 times )  of the IDIF function due to memory access re-arrangement.

Build 367 is released.

 1. Fixed crash defect : when attempting to create a REAL layer where all voxels are VOID.

2.  Fixed defect:  _isnan() function replace with _finite()

3. implement (optional) IDIF function working on the enhancement image. User has a choice

{Signal,Enchancement}

4.  Implemented IDIF dialog version : option for Input data {Signal,Enhancement}

5. Performed peformance optimization in FindMiniseed function (x2 speed improvement)

6. Added Progress indicator in FindMiniseed function that takes the majority of time.

Build 366A is released.

 1. Dynamic experiment dialog : Corrected item names to properly capitalize

2. Model #24: corrected the crash when residual layer was requested.

Build 366 is released.

 1. Dynamic parametric modelling : Made corrections in how Optimization Methods are handled. Added LLS method to the Model 24.

2. Deidentify DICOM folder : fixed defect when the files were deleted on repeated application of the procedure.

3. RoiStats3D UI function : Wait cursor is displayed so there is no perceived "hang" on larger images

4. Dynamic Modelling Global noise estimation : changed the algorithm to Diff2D.

5. Dynamic Model #24 (T1-mapping with Flip angle) : added a hyperparameter for the background expressed as the multiple of the Global Noise.

6. When F3 is pressed (on 3D image) hourglass or progress indicator  shows up. Otherwise for large volumes there was a long delay without the feedback.

7. Model 8:  Input function delay extended to the interval [Min,Max] so the negative delay (f.e. vein) could be used.

8. Set default HCT=0 in all locations except Dynamic Modelling Input Function.

9. Moved NLM-denoising to under MainMenu>Volume

Build 365B is released.

1. Dialog Concentration Conversion : when called from RoiStats4D dialog the "from DICOM" button had no effect. fixed now.

2. On the start of the Concentration Converison dialog : only the fields relevant to the starting Conversion method are enabled.

3. Fixed "Defect 12" report : from RoiStat4D dialog, the conflict between Copy To Clipboard and Save buttons when the whole concentration was turned to 0)

Build 365A is released.

 1. Dynamic Analysis>Convert 4D Volume to Concentration>Using T1-map  : Now the last dialog Concentration conversion settings are remembered between sessions.

2. Dynamic Analysis>Convert 4D Volume to Concentration>Using T1-map  : In Concentration conversion dialog the "from DICOM" button now works.

3. Concentration Conversion dialog:  fixed the defects when dialog entries would revert to their original values after pressing { LookUp Value, From DICOM}

Build 365 is released

 1. Model 24: corrected the formula appeared on the screen (no change to the code). T1-map output units are corrected to (sec)  from (ms)

2. Implemented UI-level function to construct a uniform REAL layer with specified signal and name.

This is under MainMenu>Volume>Construct Uniform layer.

3.  Implemented UI-level function to convert given 4D volume to 4D concentration volume using the voxel-wise T1-map.

 Build 364A is released.

1. Move the File>Open DICOM Series menu item to under  File>DICOM>Open selected SERIES.

Build 364 is released.

 1. Corrected various defects in the "Split Multiframe DICOM" function. Was able to load the provided CT-3D  and PET-4D files (500 and 3840 frames respectively).

2. "DICOMDIR to File Folders" : address several situations when the target folder is non-present or non-empty.  Source folder is now using the last value used for Open DICOM operation.

3. Remove "Open DICOM Series" from the main menu.

4. On the Main menu, replaced the "Open DICOM Volume...." with "Open DICOM folder..."

5. Fixed the defect, when 3D Roi is created over the 4D base volume, not able to draw. This was due to the incorrect calculation of spatial resolution (Vz=0)

6. Volume>Smooth : Enabled the floating point values for the Radius in the dialog (from INT)

7. Volume>Smooth: Corrected execution for when the source volume contains negative values.

8. Volume>Smooth (3D) : corrected so smoothing is available for REAL volumes including negative value.

9. Volume>Smooth menu item was changed to Volume>Smooth  over (optional) ROI.

Build 363A is released.

 1. Fixed a defect introduced in B363 (BlockMinMax). It was causing Signal-To-Screen Window Width to be 0.

2. Open DICOM dialog box > DELETE function : added a verify prompt to avoid accidental delete.

3. When adding a layer from file  {MIDAS,ANALYZE} and no orientation is present (VOID), there is no warning prompt and layer is seamelessly loaded.

4. Addressed a list of minor interface modifications requests.

5. Added to default PHI tags:  { OtherPatientIDs, OtherPatientIDsSequence }

Build 363 is released.

 1. REAL volumes : Upgraded internal 24-bit representation to the full REAL 64-bit representation.  Introduced new fast compression to address important situations : 

         a) Many VOIDVOX voxels

         b) REAL image was created using Nearest Neighbor scale up (f.e. in PET-MR registration            workflow).

2. Fixed a longterm defect in FrameSetBlock function when the Block buffer was improperly reallocated cutting 4 bytes off the buffer (unpredictable results in accessing uninitialized memory when displaying images),

 

3. Modified all ABT subtests to work with the new REAL representation

Build 362 is released.

 1. Added UI functionality to modify\insert b-values into SERIES or IMAGE items right from the DICOM Open dialog box.

2. Parametric Modelling dialog: fixed the error in re-creating the list of available models.

3. Parametric Modelling dialog: Implemented combo box an parameters to control optimizations.

4. Model DKI (#28) implemented the Simplex method in addition to current Global Optimization.

5. Updated and fixed the Dynamic Aggregation function (for the repeating dynamic coordinates). Provided a new ABT test for it.

6. ABT test implementation for Dynamic Aggregation.

7. Fixed the "hang" defect in Model28 while using Simplex.  Seems like hang is caused by the malloc (replaced by static buffer), which contradicts to malloc being advertised  as thread-safe.

8. Removed access to Model#12 (AATH) from the interface since it is not used and maintained at the moment.

9. Updated all dynamic models to remove the redundant optimization {GridN,Niter} parameters which are part of the standard optimization panel now.

10. Verified all the ABT subtests and regenerated new ones due to change in hyperparameters of most of the models.

 Build 361A is released

1. Cardiac Output correction dialog:  introduce CO precision parameter that controls the speed of the iterative optimization process.

2. Fixed the "time remaining" display in Cardiac Output correction processing.

3. FVX expiration date updated.

 Build 361:

1. Implemented 2 additional methods Cardiac Output-based IF correction

Build 360B is released.

 1. Volume Info dialog: displays now Transfer syntax and File Size.

2. Dialog RoiStats4D corrections:  Display extra 5% of space over the peak, show a bit more plotting area over the peak.  If Time is dynamic component it is display with no more than 2 decimals.

3. Dynamic Experiment single curve result dialog:  changed the Copy button to Report button that pops-up the Notepad and text document.

4. Dynamic Experiment single curve result dialog:  when press Report the text file contains the T1 information for each ROI present.

5. Fixed crash in  PCA-4D segmentation function

Build 360A is released.

 1. Include the message preventing saving REAL volumes to DICOM.

2. Resolve issue when the .NII.GZ file is loaded and trying to save back to .NII the .GZ extension was not recognized.

3. Dialog ROI Stats3D > Save Stats function : fixed defect in saving histogram when a void extra bin was saved at the end of histogram.

4. Dialog ROI Stats3D > Save Stats function  modified code so the the info save to a string and it writes to a file in a single write.

5. Dialog RoiStats3D : the X-axis range limits are displayed properly and are updated when they changed by User.

6. EdgeWaveLive:  fixed crash when multiple parameter changes are requested in a quick succession. This was due to the parallel nature of Windows interface so Processing was started within the existing Processing.

Build 360 is released.

1. Concentration Conversion dialog: for "No Conversion" method : disabled the Manual baseline mode,  disabled Contrast relaxivity field, enabled the HCT field. 

2. Concentration conversion method "SIGNAL" switch the interface name and source code to "No conversion" 

3. Parametric modelling Dialog:  Tissue Concentration Conversion Dialog:  HCT field is automatically set to zero and disabled (grayed).

4.   CO correction dialog: changed the naming of several fields to "Uncorrected"

5. FVX file format (v11):  now stores the Input Function Attributes, IF Concentration, Tissue Concentration settings of the current Dynamic Experiment.

6. Implemented Lookup Value button in the Concentration Conversion Dialog.  It activates the Contrast Relaxivity lookup reference table with the corresponding dialog.

7. Opening ".gz" image files  : fixed defect when either Source folder or FireVoxel folder contains spaces resulting in "File Not Found" error.

8.  Concentration Conversion dialog:  Attributes panel:  added the "from DICOM" button and corrected the behavior of Attribute fields upon saving and modelling.

9. DynamiAnalysis>CrossMutualInfo4D : Fixed crash and output appropriate diagnostics

10.  In Concentration Conversion dialog:  if this is not tissue the Two site water exchange model is disabled.

11. Updated the Model 7 (Inversion Recovery) and reconstructed the corresponding ABT subtest.

Build 359.

 1. Released first draft of FvxRad  documentation (Radiomics)

2. Radiomics 2D fixes related to VOIDVOX handling.

3. Fixed defect: when FireVoxelConfig file is empty the application crashes without starting.

4. MainMenu>ROI>Morph eliminated and subitems moved to under MainMenu>ROI>Morphology

 5. MainMenu>Register>AutoFocus with URAL removed.

6. FVX Document now have a proper "Modified" flag which is tacked correctly in all UI functions.

there was a

7. Dynamic experiment: when IF and Signal curve have different timelines, fixed mismatch between relative times for the IF curve and absolute times (since 1900) for the data curve.

 

8. Model (#8 Tofts)  exclude now all the timepoints before the contrast arrival.  This is done

by detecting first non-zero value in the modelled concentration curve.  Then residual is found starting

from that point

Build 358 is released.

 1. Radiomics output to text file is now formatted in scientific notation (1e-x)

2. Cardiac Output dialog : new option is to save the original curve in current selected concentration.

3. Extended Radiomics2D to have an option to process all the enabled (marked) ROIs at once.

4. Fixed problem when DlgRoiStat3D accessed from Radiomics2D dialog box, SaveStats function was different from one accessed directly through DlgRoiStats3D.

5. Corrected the displayed Model names for {17,18,21}

FireVoxel Build 357A is released.

 1. AIF Cardiac Output correction:  performed a fix during the iteration process which prevents a false Signal->Conc monotonity check failure.

2. AIF Cardiac Output correction:  Outputs "Time remaining" during the processing.

FireVoxel Build 357 is released.

 1.  Implemented the UserOptions option for Auto-retile document or new Views.  If unchecked,  the new View takes entire client area of the application.

2. In Parametric Modelling dialog: when Model is selected that allows only the Signal, the Tissue Concentration and IF Concentaction buttons are disabled\grayed.

3. Moved the {MagTrace,Rasterize} buttons of the main toolbar right after polyline button.

4. Implemented a notion of "VOID Image Orientation" for file formats or files when Orientation info is not present (f.e. MIDAS and sometimes ANALYZE).

5. Implemented UI function for "Set Volume Orientation".

6. Model 19: Fixed the RelPrecision error that was causing infinite loop.

    Models {7,16,17,18,44}: Removed the RelPrecision hyperparameter by setting it to default value.

7. Re-enabled Extrapolate Dynamic Dimension and made several improvements.

8. RoiStats3D dialog:   BinWidth and Range are displayed now in scientific (exponent) format.

9. Radimics dialog : changed Discretization display to scientific format.

10. Fixed : When calling Radiomics2D function with undefined discretization and setting it through RoiStats3D dialog the parameters were not properly transferred into the Radiomics function.

 Build 356 is released.

 1. MainMenu>File  :  implemented an additional function for loading DICOM files as SERIES, without constructing logical Volumes.

2. CO measurement and Correction tool : made available from the main menu under Dynamic Analysis

 

3. File>DICOM>Save Volume to Folders  option saves into the specified Folder but the files are sorted into subfolders by their respective SERIES.

4.  When DICOM Loading in "All checked items" mode additional checks for compatibility with the Volume such as {Orientation,  Slice Location} etc.

5. When Invalid FVX file contains DICOM header size=0, an appropriate diagnostics is displayed and the function orderly exits without crashing.

6.  Models {19,21,28}:   removed the Noise and RelPrecision parameters from the User Interface

7. Model {28} : Output Parameters and RMSE bounds after (global) optimization.

8. Enabled GO Solution Bounds in Monoexponential fitting.

      Model { 19,21} Output Parameters and RMSE bounds after (global) optimization.

9. Models {17,18,21} replaced the name of hyperparameter "Tail noise cutoff" with "Low signal tail cutoff"

Build 355C is released.

 1.  Save DICOM UI function (both the MainMenu>File and from LayerContol dialog) :  option pops up to generated all new random UIDs (SERIES, etc) or preserve the ones from original file.

2. DICOmM Deidentify function:   resulting files change the name to  image_XXX."original extension". Original files are deleted. Progress message now shows how many files are processed.

3.  Registration>Using Landmarks:   replaced the Affine Transform (which was previously done using Poly engine) with the explicit Affine optimization. 

Build 355B is released.

1. Made UI corrections in  Workflow>Rodent>Register to PET space.

2. CO correction tool:  fixed crash when no curve is loaded and user clicks on the plot area.

3. CO correction dialog : changed the dialog title. Removed the CLOSE (X) button which was causing the Stats notepad to show up and dialog would not close (Windows Bug?)

4.  MasterFilePresent checks avoids the expiration date check.  This allows to easily test old expired versions.

Build 355A is released.

 1. RoiStats3D dialog:  Histogram setting behavior change:

In Multilayer entity every layer volume (both Roi and Non-Roi) remember the range but keeps the track if ROI content is changed or the measure layer is different. Histogram parameters are now remembered within the ROI.

2.  FullRange button is enable only if the current range is not a FullRange.

Build 355 is released.
 

 

 1.  DICOM Tree to File Folders tool:  implemented the proper naming of Patient\Study\Series folders.

2. Verified correctness of the operation:   Load DICOM -> Save NIFTI ->Reload in the 3rd party package and display orientation correctly.  Checked out :  3D Slicer, MRIcron, ITK-SNAP all working correctly. Mango does not.

3. NIFTI load orientation:  added code for when sform>0 and qform=0. This fixes the NIFTI nih test dataset problem.

 

 

 

 

 

 

4. User Interface options dialog:

Corrected the "Posterior on Top" to "Anterior On Top"

 

 

 

5. Fixed PET-4D Dicom Load defect (mouse volumes with Non-isotropic pixel).

6. Introduced User option Projection View Convention {Original Data, Radiological, Neurological}.  This is a new option in the User Options dialog (replaces 2 previous options Right On Left }

 

 

 

 

 

 

 

 

7. WML lesion processing:  both Base2016 and V353 versions are exposed on the corresponding menu now. 

8. Fixed: When Layer Dialog box was open, after the parametric model ran it was not updated completely.  Presently, if "Process ROI only" mode isactivated the ROI is automatically disabled at the end so we can see the ParametricMap clearly. So Auto disable was not reflected in Layer Dialog.

 

9.  Model 29 (MRTM0):  changed the definition of   R₁ = −β₂/β₃.  to match the definition in Ichise paper here:  

https://journals.sagepub.com/doi/10.1097/01.WCB.0000085441.37552.CA?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub++0pubmed&

Build 354B is released.

 1. Restored the preferential Zoom\Display for the primary (natural) projection with the proper slice scrolling, FilmView etc.

2. When loading the volumes with differing X-Y resolution immediately perform conversion to X=Y resolution.

3. Expiration date reset.

4.   Info crash  problem went away after #1   was fixed.

 1. Integrated DICOM JpegLS loseless codec. Verified loading with 3D Slicer

2. User Option dialog: DICOM compression clarified JpegLS information.

3. Added support function under File>DICOM>DICOM folder Total Pixel Element size so just

the pixel info can be measured during the compression evaluation.

 

Build 354A is released.

 

 1.  CO correction dialog : Stats :  added extra measurements to the notepad document.

2.  CO correction dialog : Save :  now save the currently selected (and displayed) concentration curve.

3. CO correction dialog : Enabled the color swatch for FPC curve

Build 354 is released.

 

 1.  White Matter Lesions detection: rolled back to the original H.2016 document  version.

2.  Remove preferential optimized display of volumes when in natural projection. This fixes the display of images with unequal X-Y resolution.

Build 353 is released.

 

 1. Cardiac Output correction dialog:  added the optional display of the First Pass Curve used for calculation of the AUC in CO.

2.Modified first pass curve so the starting segment before the first non-zero concentration is interpolated by gamma variate.

3. Provided a new variant of the Gamma variate fit which guarantees that the peak of GV exactly matches the peak of the original curve.

 4. Implemented Concentration->Signal conversion for T1WR1NLC concentration method. This is required.

 5. DICOM load: enabled loading of the DICOMs with 32-bit signed\unsigned internal representation. 

6. Cardiac Output Calculation and Correction dialog:

Separated the Esimate CO and Actual CO fields for clarity.

7.  Added Stats button to the CO dialog.

 

FireVoxel Build 353 is released.

 

 1. Cardiac Output dialog parameters are now remembered between dialog restarts.

2. Made correction to the Gamma Variate fit and added the Wait Cursor.

3. AutoFocus registration:  when the single Affine Grid transformation is considered(Translation only) then the progress bar is displayed.

4.  AutoFocus final transform: fixed defect when ROI layer is tranformed the Empty color (VOIDVOX32) was incorrect and causing the empty fields getting value 1.

5. Implemented a specialized function to Uncrop kidney volume to the original FOV including ROIs.

 

         a) Load both Cropped and FFOV documents. 

         b) In FFOV documents unmark all the layers except for the main (base) layer.

         c) In Cropped document unmark all the layers except for the main (base) layer and one significant               non-empty ROI (as in screenshot). 

         d) Make the Cropped document active.

         e) Go to MainMenu>Workflow>CERENE3D>Uncrop Volume command.

         f) Dialog box will appear with all parameters set.  The only parameter that might need changing                  in the future is the Translation X,Y,Z. Default 100mm was sufficient for this example.

         g) Press OK. After some processing all the Layers of Cropped document will be transferred to the             FFOV document.

        h) Result:

 

6. Updated the Cardiac Output-based Input function correction functionality. Added the Gamma Variate fit parameter

7.  When DICOM is loaded with trivial Slope\Intercept (1\0) verification dialog does not appear anymore.

FireVoxel Build 352 is released.

 

 1. Concentration conversion dialog : Updated the parameters in the Signal Baseline panel. Items are grayed if Manual parameter not checked.

2. Gamma variate fit upgrade: provided algorithm improvement to deal when signal starts after long delay.

This works in conjunction with Concentration conversion:

In HUANK case:

User specifies the initial phase:

Gamma variate fit is properly done by skipping specified points and looking for the optimal X0 now.

3.  Gamma Variate curve is now drawn with 0.1 sec steps for more intuitive viewing. Point markers are still shown in original time.

4. Cardiac Output correction dialog box:  when the curve is not loaded all the appropriate UI documents are grayed.

5. Cardiac Output dialog \ Attributes \  opened dialog now titled Blood attributes.

Build 351A is released.

 1. White Matter lesions detection: provided algorithm update for morhological closure of Brain Mask Base. Provided UI dialog field for updating the closure value in mm.

2. RoiStats3D dialog box: when only ROI layer is present the voxel and blob count is now calculated correctly.

3. IDIF function : fixed defect when Isotropic volumes are not processed.

Build 351 is released.

 1. Implemented initial variant of UI function:  DICOM Tree to Folders.

2. Fixed crash defect in RoiStats3D dialog:  when invoking the Zigalga-threshold. 

3. DICOM Tree to File Folders:  added handlers to when Source and Target folders do not exist,

when size of the free space in the Target folder is not sufficient.

 

FireVoxel 350 is released

 1.  DICOM Deidentification :  with the response from DCMTK forum a direct solution is now possible without creating the temp files.

2.  Fixed crash defect: DlgVROI activated, grayed out and after the document closing was crashing.

3. DICOM Deidentification tool now remembers the last used folder and suggests it.

4. Removed "Close All Document" and "Close Current Document" from the MainMenu>File because they also appear under MainMenu>View.

5. Introduced FireVoxelPHIprofile :  a text file should be residing in FireVoxel application directory that lists all the DICOM tags considered to be a PHI (Protected Health Information).

6. User can view current PHI Profile by choosing MainMenu>DICOM>Show PHI profile.

 Build 349 is released.

1. Replace the custom PR_FileCopy function with Windows-based CopyFile.

2.  Modified  "Deidentify DICOM folder" function to work "in-place". User only specifies a folder and files under the folder are modified when de-identified.

3. Under both Main menus moved all DICOM functions under File>DICOM

Build 348B is released.

 1. Model #27: fixed defect when for individual voxels the message would appear "not able to find a linear fit...".

Build 348A is released.

 1. Model #27 Logan Plot: Fixed the hyper parameter mix up defect.

Build 348 is released.

 

 1.  Added a warning when *.TIME file is loaded (either with .IM or NIFTI files) and dimensions specified in TIME header are different with ones in individual pixel files.

2. Modified model #27 Logan Plot was modified to better align with the description in PMOD documentation.

3. Modified Model #27 Vt (Logan Plot) to accept reference curves with the timeline different from the image file.

4. VROI dialog: when in "none selected" mode all the buttons are disabled to avoid various crash problems.

Build 347A is released.

 1. VROI dialog box: switch default units back to voxels.

2.  VROI dialog : Restored previous Z-coordinate convention.

3. VROI MainMenu>VROI>Delete All VROIs is now the only function for deletion.

4. VROI dialog box: the changes are preserved on cancel\close the dialog box.

5. VROI dialog box:  added the UNDO button.

6. List All VROIs command now shows a scrollable list of all present VROIs (previously just a plain message box).

Build 347 is released.

 1. Implemented Cardiac Output-based input function correction tool. Full UI dialog combined with Cardiac Output measurement tool.

2. VROI selected, VK_F4 opens the RoiStats4D dialog box. The curve is now displayed in color of the selected VROI (instead of fixed Green color).

3. VROI dialog: fixed defect pressing OK button would close dialog and never being able to open again.

4. VROI dialog both OK and CANCEL buttons are gone since they are redundant. You can close VROI dialog the same way as Layer Control dialog, i.e. by clicking the "exit" button

5. VROI file now contains the color attribute for each VROI.   Old VROI files are not supported.

6. Fixed defect in DICOM Tag registration when "Document with this name is present" was incorrectly appearing.

7. Replaced several 2 button question dialogs of type "Press Yes for X, press NO for Y" with the 3 button dialogs containing Cancel button.

8. VROI dialog box: replaced the mm\vox radio button switch with the combo box.

9. VROI dialog: fixed defect that for Z0,Z1 coordinates internal 0-based coordinates were displayed. Now they are 1-based as in User-convention and also matches the info displayed in the status line.

FireVoxel Build 346 is released.

 

 1. Provided a modeless (non-Modal) version of VROI dialog box. This way VROI dialog can stay open while we do all operations with VROI, including moving and browsing (F11).

2. Changed the Dynamic index convention from [0,Ti-1] -> [1,Ti] to match the other UI convention.

3. Changed the panel from Time to Dynamic Index 

 

 

4. Changed the diagnostics message when the FVX license file is missing.

5.  Show Main Toolbar command is now available from Main Menu when documents are opened.

6. Fixed the issues around the Insert Polyline (freehand) menu items.

7. Fixed defect in "Vector rasterize" when the previous content of the working ROI layer was overdrawn and disappeared.

8. Remove Mainframe>Test menu item from the Release versions.

9. Rasterization functions:  fixed Redraw problem due to parallel access of the ZoomCache.

FireVoxel Build 345E was released.

 1.  List all VROIs:  removed  "visible\invisible" status info.

2.  When VROI is created - it is assigned a default name  "vroi index", where index is the count

of VROIs previously created.

3. Moved VROI>3D to 4D to under MainMenu>ROI.

4. Moved VROI>Optimal zoom to  MainMenu>ROI>Zoom whole extent.

5. Fixed crash in Volume>Noise>Median Noise.

6. When ROI layer is created by any operation its DICOM headers are immediately and automatically minimized.

Build 345D is released.

 1. Corrected Gauss Downscale when the Single slice volume is transformed into single slice.

2. Restored the "diagonal cross" in VROIs, increased transparency.

3. "Create orthogonal projections"  : disallowed creating the repeating redundant projections.

4. In Multilayer entity, after removing one or more layers - the base layer becomes transparent.

 Build 345C is released.

 1. Transform>Volume Rotation dialog : Added the "Gaussian Downscale" option.

2.  Batch transform using task file:  replaced old interpolation radio buttons with common combo box.

3. Transform using VTF file dialog:  replaced old interpolation radio buttons with common combo box.

 

4. Fixed defect in BiCal batch processing:  when several subfolders of the Source folder were not processed.

 FireVoxel Build 345B

1.  Corrected the folder construction in BiCal Batch processing.