Hello,
I encountered an issue when using the Pencil tool in Segment Editor. On some slices and with certain datasets, the pencil strokes are not visible in the 2D views (axial/sagittal/coronal). However, in the 3D view it is clear that the segmentation is actually being created.
Steps to reproduce:
1. Load a volume (.mhd in my case)
2. Open Segment Editor
3. Use the Pencil tool on different slices
Expected behavior:
The drawn segmentation should be visible in 2D slice views while drawing.
Actual behavior:
On some slices/files, the pencil is not visible in 2D views, although it appears correctly in 3D.
Version: Slicer 5.10.0 (rev 34045)
Any ideas what might be causing this?
Thanks.
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - Session start time …: 20260503_095834
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - Slicer version …: 5.10.0 (revision 34045 / a2b6d08) macosx-amd64 - installed release
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - Operating system …: macOS / 26.4.1 / 25E253 / UTF-8 - 64-bit
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - Memory …: 8192 MB physical, 2048 MB virtual
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - CPU …: Apple M2, 8 cores, 8 logical processors
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - Qt configuration …: version 5.15.18, with SSL, requested OpenGL 3.2 (core profile)
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - DCMTK configuration …: version 3.6.8, no SSL
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - Internationalization …: disabled, language=
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - Developer mode …: disabled
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - Application path …: /Applications/Slicer.app/Contents/MacOS
[DEBUG][Qt] 03.05.2026 09:58:34 (unknown:0) - Additional module paths ..: (none)
[INFO][Stream] 03.05.2026 09:58:35 (unknown:0) -
[DEBUG][Python] 03.05.2026 09:58:38 [Python] (/Applications/Slicer.app/Contents/lib/Slicer-5.10/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 03.05.2026 09:58:38 [Python] (/Applications/Slicer.app/Contents/lib/Slicer-5.10/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 03.05.2026 09:58:38 (unknown:0) - Switch to module: “Welcome”
[DEBUG][Qt] 03.05.2026 09:58:59 (unknown:0) - “Volume” Reader has successfully read the file “/Users/alexanderschirkow/Downloads/SITE_006_PAT_007/vibe963_q_dixon_tra_p4_bh_DL_FF_Series0103.mhd” “[0.12s]”
[DEBUG][Qt] 03.05.2026 09:58:59 (unknown:0) - “Volume” Reader has successfully read the file “/Users/alexanderschirkow/Downloads/SITE_006_PAT_007/vibe963_q_dixon_tra_p4_bh_DL_R2s_Eff_Series0105.mhd” “[0.04s]”
[DEBUG][Qt] 03.05.2026 09:58:59 (unknown:0) - “Volume” Reader has successfully read the file “/Users/alexanderschirkow/Downloads/SITE_006_PAT_007/vibe963_q_dixon_tra_p4_bh_DL_W_Series0101.mhd” “[0.03s]”
[DEBUG][Qt] 03.05.2026 09:59:11 (unknown:0) - Switch to module: “Data”
[DEBUG][Qt] 03.05.2026 09:59:18 (unknown:0) - Switch to module: “SegmentEditor”
[INFO][Stream] 03.05.2026 10:10:52 (unknown:0) - self.extentGrowthRatio = 0.1
[INFO][Stream] 03.05.2026 10:10:52 (unknown:0) - masterImageExtent = (0, 319, 0, 279, 0, 71)
[INFO][Stream] 03.05.2026 10:10:52 (unknown:0) - labelsEffectiveExtent = (68, 217, 91, 203, 4, 63)
[INFO][Stream] 03.05.2026 10:10:52 (unknown:0) - labelsExpandedExtent = [54, 231, 80, 214, 0, 68]
[DEBUG][Qt] 03.05.2026 10:16:43 (unknown:0) - Switch to module: “Segmentations”
[DEBUG][Qt] 03.05.2026 10:16:47 (unknown:0) - Switch to module: “SegmentEditor”
[INFO][Stream] 03.05.2026 10:27:58 (unknown:0) - self.extentGrowthRatio = 0.1
[INFO][Stream] 03.05.2026 10:27:58 (unknown:0) - masterImageExtent = (0, 319, 0, 279, 0, 71)
[INFO][Stream] 03.05.2026 10:27:58 (unknown:0) - labelsEffectiveExtent = (68, 263, 90, 203, 4, 63)
[INFO][Stream] 03.05.2026 10:27:58 (unknown:0) - labelsExpandedExtent = [49, 282, 79, 214, 0, 68]
[DEBUG][Qt] 03.05.2026 10:30:04 (unknown:0) - Switch to module: “Markups”
[DEBUG][Qt] 03.05.2026 10:32:19 (unknown:0) - Switch to module: “SegmentEditor”
[DEBUG][Qt] 03.05.2026 10:33:08 (unknown:0) - Switch to module: “Data”
[DEBUG][Qt] 03.05.2026 12:12:24 (unknown:0) - “Volume” Reader has successfully read the file “/Users/alexanderschirkow/Downloads/SITE_006_PAT_008/vibe963_q_dixon_tra_p4_bh_DL_FF_Series0103.mhd” “[0.15s]”
[DEBUG][Qt] 03.05.2026 12:12:24 (unknown:0) - “Volume” Reader has successfully read the file “/Users/alexanderschirkow/Downloads/SITE_006_PAT_008/vibe963_q_dixon_tra_p4_bh_DL_R2s_Eff_Series0105.mhd” “[0.04s]”
[DEBUG][Qt] 03.05.2026 12:12:24 (unknown:0) - “Volume” Reader has successfully read the file “/Users/alexanderschirkow/Downloads/SITE_006_PAT_008/vibe963_q_dixon_tra_p4_bh_DL_W_Series0101.mhd” “[0.03s]”
[DEBUG][Qt] 03.05.2026 12:12:37 (unknown:0) - Switch to module: “SegmentEditor”