Slicer4 - Change Log

0004445: [Core: Base Code] Model files should be saved in LPS coordinate system (lassoan) 0004699: [Core: Documentation and Wiki] VolumeRendering: Update documentation to describe multivolume support (pinter) 0004612: [Core: Building (CMake, Superbuild)] Build error with GCC/G++ 8.2.0 (jcfr) 0004718: [Core: Base Code] Compile error without WebEngine Support (sankhesh) 0004710: [Module Markups] Remove All Markups button doesn't update Markups module table (lassoan) 0004464: [Module Models] Scalar overlays: Displayed range not restored when loading saved scene (lassoan) 0004616: [Core: Building (CMake, Superbuild)] Build error with GCC 8.2.0 within libarchive (jcfr) 0004022: [Module DICOM] Default DICOM database directory might not be writable (pieper) 0004713: [Module SubjectHierarchy] Subject hierarchy hangs if script sets child item as parent of its parent (pinter) 0004712: [Core: Base Code] Slicer fails to start in Intel Ivy Bridge or older CPUs (lassoan) 0004709: [Module DICOM] need to escape apostrophe in sql statement (pinter) 0004663: [Module Segment Editor] Traceback error while using Fill Between Slices auto-complete (pinter) 0004694: [Module Markups] Slicer crashes when deleting Markups node (lassoan) 0004670: [Core: Extensions] QFormBuilder unable to create extension custom widgets (arankin) 0004689: [Module Markups] Markup labels not always visible in tall views (jcfr) 0004560: [Core: Base Code] C++11: Modernize NULL and 0 to nullptr (jcfr) 0003482: [Module Volumes] Combobox arrows in Image Dim/Spacing/Origin fields have no effect (lassoan) 0001915: [Core: Base Code] Effect of matrix bottom row in Transforms module (jcfr) 0004687: [Module Segment Editor] Fill between slices broken (lassoan) 0004684: [Core: Segmentation] Crash while selecting "Segmentation" as file type for a label (pinter) 0004668: [Module (Any modules)] Sample Data module will not load custom sample data with filetype MRB 0004654: [Core: Usability] XCode required to use Slicer on mac (pieper) 0003262: [Module DataProbe] Data probe panel is not updated when scrolling volume slices using keyboard (pieper) 0002777: [Core: GUI] Left mouse button changes W/L in the slice viewers (lassoan) 0004658: [Core: GUI] Make terminology navigator easier to use (pinter)

0004634: [Module LandmarkRegistration] Most fiducials not selectable in LandmarkRegistration with latest VTK (sjh267) 0004671: [Core: Base Code] Backport (sjh267)

0004659: [Module SubjectHierarchy] Segment convenience functions in subject hierarchy (pinter) 0004618: [Module Extension Wizard] Extension Wizard should give more informative error message about git requirement (lassoan) 0004586: [Core: Scripting (Wrapping, Python)] Bundle pip.exe in Slicer installer (jcfr) 0004653: [Module DICOM] Button row in DICOM browser cut off on windows (pieper) 0004401: [Module SubjectHierarchy] Improve subject hierarchy transform handling (pinter)

0004327: [Module VolumeRendering] Please consider implementing a "lock" for various settings in the VR module (pinter) 0002708: [Core: Building (CMake, Superbuild)] Gatekeeper - Mac OSX 10.8 - Can't open because it s from an unidentified developer (jcfr)

0004340: [Core: Base Code] Impossible to use Slicer in multi-user setting on Linux (jcfr) 0004592: [Core: Extensions] Additional Module paths fail to import path issue (jcfr) 0004567: [Core: Base Code] DataStore module does not download any data (jcfr) 0004513: [Core: Rendering] VTK OpenGL2 Backend: Problem with volume rendering surface gradient computation (sankhesh) 0004641: [Core: Extensions] Disable extension auto-update support (jcfr) 0004522: [Core: Base Code] ITK should be built with ITK_LEGACY_REMOVE set to ON (jcfr) 0004636: [Core: Building (CMake, Superbuild)] Unable to import VTK in Windows nightly build (jcfr) 0004578: [Core: Building (CMake, Superbuild)] Update VTK external project to include up-to-date VTK (jcfr) 0004638: [Core: Extensions] Fix Qt WebEngine locales and ICU data not found when opening extension manager on Linux (jcfr) 0004544: [Core: Base Code] Unable to launch Extension Manager in Slicer-4.9.0-2018-04-19 (jcfr) 0002189: [Core: Scripting (Wrapping, Python)] Embed IPython (jcfr) 0003069: [Module VolumeRendering] Render multiple volumes simulatenously in the same view (finetjul) 0004630: [Core: Building (CMake, Superbuild)] Rename VTK external project from External_VTKv9 to External_VTK (jcfr) 0004633: [Core: GUI] Fix qSlicerReformatModuleWidgetGenericTest by ensuring ctkDoubleSpinBox sizeHint is valid (jcfr) 0004631: [Core: Base Code] Fix CTKAppLauncherLib link error (jcfr) 0004623: [Core: Building (CMake, Superbuild)] Adapt to VTK version update from 9.0 to 8.2 (jcfr) 0004625: [Module EMSegment] EMSegment not functioning, should be removed (sjh267) 0004605: [Core: Base Code] Finalize CTKAppLauncher update (jcfr)       0004595: [Core: Building (CMake, Superbuild)] multiple rules generate slicer (ninja error) (jcfr) 0004551: [Core: Extensions] Manage Extension: Can not come back to listing (jcfr) 0004619: [Extension: (Any extensions)] Hardcoded video length limit of 30 s is too low in ScreenCapture.py (lassoan) 0004552: [Core: Extensions] Extension Manager: External link do NOT work (jcfr) 0004613: [Extension: (Any extensions)] Extension manager buttons not accessible (sjh267) 0004607: [Core: Base Code] Linux: Failed to load CTK plugin when using nightly build for r27399 (jcfr) 0004615: [Core: Rendering] VTK OpenGL2 Backend: Warnings about error in cache state for GL_SCISSOR_TEST (jcfr) 0004600: [Core: Rendering] VTK OpenGL2 Backend: Toggling surface smoothing hide/show GPU volume rendering instead of effectively updating the smoothing (allison.vacanti) 0004609: [Module VolumeRendering] VTK OpenGL2 Backend: ROI widget sides are completely opaque if depth peeling is enabled (allison.vacanti) 0004542: [Module SceneViews] Scene Views crashes Slicer (lassoan) 0004598: [Core: Rendering] VTK OpenGL2 Backend: Enabling Volume Rendering module breaks viewers (jcfr) 0004510: [Core: Rendering] VTK OpenGL2 Backend: Cropping is broken with GPU Volume rendering if depth peeling is enabled (allison.vacanti) 0004548: [Core: Rendering] VTK OpenGL2 Backend: Volume rendering artifacts at volume edges when clipped (allison.vacanti) 0004308: [Core: Segmentation] Add convenient GUI for changing segmentation labelmap geometry (pinter) 0004410: [Core: Segmentation] Changing master volume in SegmentEditor does not update edit-able FOV (pinter) 0004571: [Core: Documentation and Wiki] Build instruction need to be updated for Qt5/VTK9 (jcfr) 0004521: [Module VolumeRendering] Add reset volume rendering preset to default (pinter) 0004080: [Module Transforms] Transform module is not updated properly after importing a scene (jcfr) 0003806: [Module DICOM] Imported DICOM file does not show up in widget under certain conditions (nicole) 0004568: [Extension: (Any extensions)] Elastix General registration will not run (lassoan) 0004242: [Core: Testing Infrastructure] Testing of scripted module that depend on loadable module fails (jcfr) 0004533: [Module SimpleFilters] Incorrect(?) future warning message for simple ITK (blowekamp) 0003929: [Core: Rendering] 3d visualization of image slice does not go through the middle of VR slice (jcfr) 0003667: [Module Transforms] Applying a non-linear transform creates an empty image if the displacement is large (lassoan) 0004566: [Core: Building (CMake, Superbuild)] Fix -Woverloaded-virtual warning in vtkITKImageThresholdCalculator.cxx (phcerdan) 0004471: [Core: Scripting (Wrapping, Python)] Slicer does not parse the python script path correctly (lassoan) 0004563: Ctrl-W "Close Scene" looses all data (lassoan) 0004511: [Core: Rendering] OpenGL2: Large camera view angle (used in OpenVR) not properly handled with GPU Volume Rendering (sankhesh) 0001752: [Module VolumeRendering] volume rendering is adaptive, even if the quality control is set to maximum (finetjul) 0004485: [Core: Base Code] Unsafe call in vtkMRMLModelDisplayNode::GetOutputMesh (jcfr) 0004064: [Module VolumeRendering] Slicer (volume rendering module) cannot start with an Nvidia driver version (finetjul) 0003450: [Module VolumeRendering] VR Module issues (pinter) 0004293: [Core: Rendering] VTK GPU Ray Casting fails in SLicer 4.6.0. in Windows 10 with NVidia GTX960M (latest driver) (jcfr) 0003562: [Core: GUI] Volume Rendering - Transfer Function (lassoan) 0001996: [Module VolumeRendering] the vtk gpu raycaster does not render in full quality (lassoan) 0004497: [Core: Rendering] Rendering block/freeze the GUI if the startup layout has not both a 3D and 2D view LINUX QT5/VTK9 (lassoan) 0004423: [Core: Rendering] VTK OpenGL2 Backend: Slow slice scrolling if volume rendering is enabled (lassoan) 0004535: [Module SimpleFilters] Slicer crash when searching in the SimpleFilters module (blowekamp) 0004536: [Core: GUI] Closed pop-up dialogs still shown in taskbar thumbnail preview (lassoan) 0004547: [Module VolumeRendering] Volume rendering with ROI cropping - MRML scene backwards compatibility issue (pinter) 0004526: [Core: GUI] Procedural color node points may be dragged out of visible range (pinter) 0004517: [Core: Base Code] macOS: Slicer dmg installer and Slicer app do not have the icon (jcfr) 0004512: [Module Markups] Fiducials not updated when placed in the 3D view in Persistent mode (lassoan) 0004409: [Module DICOM] CT images acquired with gantry tilt are loaded incorrectly (pieper) 0003951: [Core: Rendering] VTK OpenGL2 Backend: GPU VR - Slower than CPU VR (aashish24) 0002697: [Core: Building (CMake, Superbuild)] Associated publisher to windows NSIS installer - signing of package/application (jcfr) 0003967: [Core: Rendering] VTK OpenGL2 Backend: Slicer crash when switching from CPU to GPU rendering when running on vmware fusion (aashish24) 0004016: [Core: Documentation and Wiki] Wiki is missing Registration introduction (jcfr) 0002779: [Core: Extensions] Mechanism to keep track of the installed extensions across version (jcfr) 0002972: [Module MultiVolume Exporter/Importer] Support loading multivolumes from 4D NRRD/NIFTI (fedorov) 0003406: [Core: MRML] Saved scene file is corrupted if a node name contains special character (lassoan) 0004433: [Module Transforms] Harden non-linear transform may clip volume (lassoan) 0004516: [Core: Rendering] Slicer hangs if volume rendering is initiated in 3D-only layout (lassoan) 0004134: [Core: Building (CMake, Superbuild)] Upgrade to Qt 5.x (jcfr) 0004501: [Core: GUI] Qt5 smaller icons (johan.andruejol) 0004479: [Core: Chart] Qt5 : crash on application closure if ChartView has been shown (johan.andruejol) 0004125: [Core: Base Code] Linux crash at startup on fresh build (jcfr) 0004460: [Core: Documentation and Wiki] Terminologies Module: Create wiki page (pinter) 0004463: [Module DicomToNrrdConverter] Cannot convert DWI Nifti to NRRD (inorton) 0004452: [Core: Base Code] numpy build error - looks for fortran compiler (jcfr) 0004628: [Module Markups] Unable to move fiducial position with cursor (jcfr) 0004632: [Core: Base Code] py_LandmarkRegistration test segfault (pieper) 0003728: [Core: Extensions] Fix crash in qMidasAPI.cpp (sjh267) 0004569: [Core: Segmentation] Normals are flipped when smoothing factor is 0 (pinter) 0004546: [Core: Usability] Dot (".") in volume name leads to wrong variable name, wrong modified status, and suffix doubling (lassoan) 0004532: [Core: GUI] Slicer crashes when using "Add" or "Subtract" for blending (lassoan) 0003831: [Core: Packaging] Add rpath to all executable bundled in Slicer.app/Contents/bin (jcfr) 0004553: [Core: Packaging] SlicerPython does not launch with packaged SlicerPythonLauncherSettings.ini configuration (jcfr) 0004554: [Core: Packaging] rpath not set for macOS binaries in 4.9.0 (jcfr) 0004556: [Core: Packaging] PYTHONPATH in SlicerPythonLauncherSettings.ini needs additional paths to import vtk in SlicerPython (jcfr) 0004370: [Core: Segmentation] Allow reordering of segments (pinter) 0004462: [Core: Scripting (Wrapping, Python)] Python wrapping of VTK classes in extensions does not work properly (jcfr) 0004530: [Core: GUI] Qt5: Slice viewer are too small after switching to conventional layout (jcfr) 0004518: [Module Transforms] Slicer crashes when clicking on Transforms color widget (pinter) 0004515: [Core: Base Code] Style plugin not loaded in macOS installer (jcfr) 0004493: [Module SimpleFilters] crash In ‘Filtering/Threshold scalar volume’ module (lassoan) 0004503: [Core: GUI] Empty popup dialog and on Slicer startup with Qt5 (johan.andruejol) 0001585: [Core: GUI] Checkboxes in qMRMLCheckableNodeComboBox are invisible (pinter) 0004456: [Core: GUI] Qt5: QComboBox becomes empty after selection changed (pinter) 0004495: [Core: GUI] Qt5 Fiducial/ROI/Ruler icons duplicating (lassoan) 0004313: [Module SubjectHierarchy] Move edited segmentation to the study of the master volume (pinter) 0004474: [Module DICOM] TypeError in DICOMUtils (pinter) 0004360: [Module DICOM] Two popups after DICOM import (pieper)

0003812: [Module VolumeRendering] Fix -Waggressive-loop-optimizations - undefined behavior warning in vtkSlicerGPURayCastMultiVolumeMapper (finetjul) 0003811: [Module VolumeRendering] Fix -Wmaybe-uninitialized warning in vtkSlicerFixedPointVolumeRayCastCompositeGOHelper (finetjul) 0004001: [Module DICOM] DICOM import failure due to incorrect database directory (mehrtash) 0003865: [Core: Base Code] Save does not work for DICOM images (jcfr) 0004264: [Core: Segmentation] Unable to quantify left atrial fibrosis (lassoan) 0004288: [Core: Segmentation] Slicer crashes during application exit if a Segment Editor effect is active (pinter) 0004391: [Core: Segmentation] Problems loading and rendering segmentations (pinter) 0004468: [Core: Base Code] Slicer3D 4.8 (jcfr) 0004262: [Core: Segmentation] Segmentation export into labelmap after Segment color changed, remains the same color as used for painting (lassoan) 0004265: [Core: Segmentation] Undo / redo doesn't work when deleting a segment (lassoan) 0004283: [Core: Segmentation] Not possible to export surface created in Segment Editor (lassoan) 0004274: [Core: Segmentation] Slice interpolation access (lassoan)