nnInteractive module no longer segments properly

lukejprose
Mon, 26 Jan 2026 10:34:37 +0000
Support

I have been using the nnInteractive module through MorphoCloud to segment CT scans of fish skulls, with a good bit of success. Now, however, the nnInteractive module no longer functions properly. The Configuration tab says that the server is reachable, but when placing the first positive point on one of the slices, it generates a cube that does not render in 3D space. Placing any additional points results in nothing happening. I have tried closing and reopening 3D Slicer, restarting the server in the terminal, changing the server port, deleting and reinstalling the nnInteractive server, logging in and out of MorphoCloud, shelving and unshelving the MorphoCloud Instance, and redoing my mrb file. Nothing fixes the issue. Even after updating the nnInteractive extension to the latest version, it still has the same issue.

3D Slicer - Log File:

[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - Session start time …: 20260125_213237
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - Slicer version …: 5.10.0 (revision 34045 / a2b6d08) linux-amd64 - installed release
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - Operating system …: Linux / 6.8.0-90-generic / #91~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 20 15:20:45 UTC 2 / UTF-8 - 64-bit
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - Memory …: 60263 MB physical, 0 MB virtual
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - CPU …: AuthenticAMD AMD EPYC-Milan Processor, 16 cores, 16 logical processors
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - Qt configuration …: version 5.15.2, with SSL, requested OpenGL 3.2 (core profile)
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - DCMTK configuration …: version 3.6.8, no SSL
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - Internationalization …: disabled, language=
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - Developer mode …: disabled
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - Application path …: /media/volume/MyData/Slicer/bin
[DEBUG][Qt] 25.01.2026 21:32:37 (unknown:0) - Additional module paths ..: slicer.org/Extensions-34045/SegmentEditorExtraEffects/lib/Slicer-5.10/qt-loadable-modules, slicer.org/Extensions-34045/SegmentEditorExtraEffects/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/SurfaceMarkup/lib/Slicer-5.10/qt-loadable-modules, slicer.org/Extensions-34045/SlicerMorph/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/MarkupsToModel/lib/Slicer-5.10/qt-loadable-modules, slicer.org/Extensions-34045/SurfaceWrapSolidify/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/Photogrammetry/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/MorphoDepot/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/DenseCorrespondenceAnalysis/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/Sandbox/lib/Slicer-5.10/qt-loadable-modules, slicer.org/Extensions-34045/Sandbox/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/SlicerBiomech/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/ScriptEditor/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/ModelToModelDistance/lib/Slicer-5.10/cli-modules, slicer.org/Extensions-34045/NNInteractive/lib/Slicer-5.10/qt-scripted-modules
[INFO][Stream] 25.01.2026 21:32:37 (unknown:0) -
[WARNING][Qt] 25.01.2026 21:32:45 (unknown:0) - libpng warning: iCCP: profile ‘ICC Profile’: ‘CMYK’: invalid ICC profile color space
[DEBUG][Python] 25.01.2026 21:32:46 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/git/cmd.py:1253) - Popen([‘git’, ‘version’], cwd=/home/exouser, stdin=None, shell=False, universal_newlines=False)
[DEBUG][Python] 25.01.2026 21:32:46 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/git/cmd.py:1253) - Popen([‘git’, ‘version’], cwd=/home/exouser, stdin=None, shell=False, universal_newlines=False)
[WARNING][Qt] 25.01.2026 21:32:46 (unknown:0) - libpng warning: iCCP: known incorrect sRGB profile
[DEBUG][Python] 25.01.2026 21:32:47 [Python] (/media/volume/MyData/Slicer/lib/Slicer-5.10/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 25.01.2026 21:32:47 [Python] (/media/volume/MyData/Slicer/lib/Slicer-5.10/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 25.01.2026 21:32:47 (unknown:0) - Switch to module: “Welcome”
[DEBUG][Python] 25.01.2026 21:32:48 [Python] (/media/volume/MyData/Slicer/lib/Slicer-5.10/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: FormatMarkups
[INFO][Python] 25.01.2026 21:32:48 [Python] (:3) - Adding SlicerMorph Volume Rendering Presets
[DEBUG][Python] 25.01.2026 21:32:48 [Python] (/media/volume/MyData/Slicer/lib/Slicer-5.10/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SavePyFile
[DEBUG][Qt] 25.01.2026 21:32:48 (unknown:0) - bool qSlicerSubjectHierarchyPluginHandler::registerPlugin(qSlicerSubjectHierarchyAbstractPlugin*) : SubjectHierarchy plugin “SavePyFile” is already registered
[DEBUG][Qt] 25.01.2026 21:35:39 (unknown:0) - Switch to module: “SlicerNNInteractive”
[WARNING][Qt] 25.01.2026 21:35:40 (unknown:0) - QLayout::addChildLayout: layout “” already has a parent
[WARNING][Qt] 25.01.2026 21:35:40 (unknown:0) - QLayout::addChildLayout: layout “” already has a parent
[DEBUG][Python] 25.01.2026 21:35:43 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:241) - Starting new HTTP connection (1): 0.0.0.0:1527
[DEBUG][Python] 25.01.2026 21:35:43 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:544) - http://0.0.0.0:1527 “GET / HTTP/1.1” 404 22
[DEBUG][Python] 25.01.2026 21:35:45 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:241) - Starting new HTTP connection (1): 0.0.0.0:1527
[DEBUG][Python] 25.01.2026 21:35:45 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:544) - http://0.0.0.0:1527 “GET / HTTP/1.1” 404 22
[ERROR][VTK] 25.01.2026 21:36:16 [vtkMRMLSliceNode (0x1998ce10)] (vtkMRMLSliceNode.cxx:357) - GetSliceOrientationPreset: invalid orientation preset name: Reformat
[ERROR][VTK] 25.01.2026 21:36:16 [vtkMRMLSliceNode (0x19842b90)] (vtkMRMLSliceNode.cxx:357) - GetSliceOrientationPreset: invalid orientation preset name: Reformat
[ERROR][VTK] 25.01.2026 21:36:16 [vtkMRMLSliceNode (0x1984df30)] (vtkMRMLSliceNode.cxx:357) - GetSliceOrientationPreset: invalid orientation preset name: Reformat
[DEBUG][Qt] 25.01.2026 21:36:18 (unknown:0) - “MRB Slicer Data Bundle” Reader has successfully read the file “/media/volume/MyData/Betta 3D Data/Betta-tomi_01_cas-su_69819/2026-01-22-Scene.mrb” “[11.10s]”
[WARNING][Qt] 25.01.2026 21:36:32 (unknown:0) - ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 1 1
[DEBUG][Python] 25.01.2026 21:37:11 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:241) - Starting new HTTP connection (1): 0.0.0.0:1527
[DEBUG][Python] 25.01.2026 21:37:18 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:544) - http://0.0.0.0:1527 “POST /upload_image HTTP/1.1” 200 15
[DEBUG][Python] 25.01.2026 21:37:28 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:241) - Starting new HTTP connection (1): 0.0.0.0:1527
[DEBUG][Python] 25.01.2026 21:37:39 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:544) - http://0.0.0.0:1527 “POST /upload_segment HTTP/1.1” 200 15
[DEBUG][Python] 25.01.2026 21:37:39 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:241) - Starting new HTTP connection (1): 0.0.0.0:1527
[DEBUG][Python] 25.01.2026 21:37:53 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:544) - http://0.0.0.0:1527 “POST /add_point_interaction HTTP/1.1” 200 124096
[DEBUG][Python] 25.01.2026 21:38:24 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:241) - Starting new HTTP connection (1): 0.0.0.0:1527
[DEBUG][Python] 25.01.2026 21:38:29 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:544) - http://0.0.0.0:1527 “POST /upload_segment HTTP/1.1” 200 15
[DEBUG][Python] 25.01.2026 21:38:29 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:241) - Starting new HTTP connection (1): 0.0.0.0:1527
[DEBUG][Python] 25.01.2026 21:38:31 [Python] (/media/volume/MyData/Slicer/lib/Python/lib/python3.12/site-packages/urllib3/connectionpool.py:544) - http://0.0.0.0:1527 “POST /add_point_interaction HTTP/1.1” 200 155758
[DEBUG][Qt] 25.01.2026 22:12:07 (unknown:0) - Switch to module: “Reformat”
[INFO][Stream] 25.01.2026 22:12:10 (unknown:0) - onSliceVisibilityChanged
[INFO][Stream] 25.01.2026 22:12:14 (unknown:0) - onSliceVisibilityChanged
[DEBUG][Qt] 25.01.2026 22:12:16 (unknown:0) - Switch to module: “SlicerNNInteractive”

12 posts - 2 participants