# 3D Slicer Paint/Draw Tool Issue 

**URL:** <https://discourse.slicer.org/t/3d-slicer-paint-draw-tool-issue/32531>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [November 1, 2023, 8:12pm UTC](https://discourse.slicer.org/t/3d-slicer-paint-draw-tool-issue/32531 "2023-11-01T20:12:54Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Cameron\_Shepherd](https://avatars.discourse-cdn.com/v4/letter/c/65b543/32.png) [@Cameron\_Shepherd](https://discourse.slicer.org/u/Cameron_Shepherd)\
**Post date:** [November 1, 2023, 8:12pm UTC](https://discourse.slicer.org/t/3d-slicer-paint-draw-tool-issue/32531/1 "2023-11-01T20:12:54Z")

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Operating system: Windows 11  
Slicer version: 5.0.3  
Background:  
I am a undergraduate working within a research lab and I have been using 3D Slicer for about a year now. This issue is with the paint tool and has happened previously but a reset from the pc I work on would typically fix it, however that fix did not work. I use the paint/draw tool to create segments within a CT scan of cavefish brains and to ensure the segments are “right”, I am given the proper image spacing for each cluster of scanned individuals. After I ID the proper voxel size for xyz, I place that within the image spacing tab as I was taught.

Expected behavior:  
Typical behavior for the paint tool would be to use circles as a “base” to trace/highlight certain sections I want within the CT scan and transform the highlighted area into a segment that is selected.

Actual behavior:  
Instead of the “base” use of a circle to trace/outline what I want on the CT scan, the tool is creating squares across the entire scan. This behavior is happening across multiple CT scans of the same individual and other individuals. I have also figured out the voxel spacing value, when placing within the image spacing within the volumes tab, can cause the issue to happen artificially.

I have attached screenshots and the log messages for today. I replicated the issue multiple times over and over.

Log Messages:  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - Session start time …: 2023-11-01 13:49:42  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - Slicer version …: 5.0.3 (revision 30893 / 7ea0f43) win-amd64 - installed release  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - Operating system …: Windows / Professional / (Build 22000, Code Page 65001) - 64-bit  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - Memory …: 32559 MB physical, 37423 MB virtual  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - CPU …: GenuineIntel , 24 cores, 24 logical processors  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - Qt configuration …: version 5.15.2, with SSL, requested OpenGL 3.2 (compatibility profile)  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - Internationalization …: disabled, language=  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - Developer mode …: disabled  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - Application path …: C:/Users/DLC/AppData/Local/NA-MIC/Slicer 5.0.3/bin  
[DEBUG][Qt] 01.11.2023 13:49:42 (unknown:0) - Additional module paths …: NA-MIC/Extensions-30893/SegmentEditorExtraEffects/lib/Slicer-5.0/qt-loadable-modules, NA-MIC/Extensions-30893/SegmentEditorExtraEffects/lib/Slicer-5.0/qt-scripted-modules, NA-MIC/Extensions-30893/MarkupsToModel/lib/Slicer-5.0/qt-loadable-modules, NA-MIC/Extensions-30893/SlicerMorph/lib/Slicer-5.0/qt-scripted-modules  
[WARNING][Qt] 01.11.2023 13:49:46 (unknown:0) - libpng warning: iCCP: profile ‘ICC Profile’: ‘CMYK’: invalid ICC profile color space  
[WARNING][Qt] 01.11.2023 13:49:47 (unknown:0) - libpng warning: iCCP: known incorrect sRGB profile  
[DEBUG][Python] 01.11.2023 13:49:48 [Python] (C:\Users\DLC\AppData\Local\NA-MIC\Slicer 5.0.3\lib\Slicer-5.0\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: Annotations  
[DEBUG][Python] 01.11.2023 13:49:49 [Python] (C:\Users\DLC\AppData\Local\NA-MIC\Slicer 5.0.3\lib\Slicer-5.0\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentEditor  
[DEBUG][Python] 01.11.2023 13:49:49 [Python] (C:\Users\DLC\AppData\Local\NA-MIC\Slicer 5.0.3\lib\Slicer-5.0\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentStatistics  
[DEBUG][Python] 01.11.2023 13:49:49 [Python] (C:\Users\DLC\AppData\Local\NA-MIC\Slicer 5.0.3\lib\Slicer-5.0\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: FormatMarkups  
[DEBUG][Qt] 01.11.2023 13:49:49 (unknown:0) - Switch to module: “Welcome”  
[DEBUG][Qt] 01.11.2023 13:49:49 (unknown:0) - Local filepath received via command-line: “E:\DLC\Documents\Harvard\09212022\Contrast\Holtz\_asty3\_I [2022-10-11 18.43.06]\ZStacks\Crop\Row\_4\72\Holtz\_asty3\_I\_0276.jpg”  
[ERROR][VTK] 01.11.2023 13:49:50 [vtkITKArchetypeDiffusionTensorImageReaderFile (00000252B99ED3F0)] (D:\D\S\S-0\Libs\vtkITK\vtkITKArchetypeDiffusionTensorImageReaderFile.cxx:166) - There is more than one file, use the vtkITKArchetypeImageSeriesReader instead  
[INFO][VTK] 01.11.2023 13:49:50 [vtkMRMLVolumeArchetypeStorageNode (00000252B9D6C0B0)] (D:\D\S\S-0\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx:513) - Loaded volume from file: E:/DLC/Documents/Harvard/09212022/Contrast/Holtz\_asty3\_I [2022-10-11 18.43.06]/ZStacks/Crop/Row\_4/72/Holtz\_asty3\_I\_0276.jpg. Dimensions: 419x389x229. Number of components: 3. Pixel type: unsigned char.  
[DEBUG][Qt] 01.11.2023 13:49:50 (unknown:0) - “Volume” Reader has successfully read the file “E:/DLC/Documents/Harvard/09212022/Contrast/Holtz\_asty3\_I [2022-10-11 18.43.06]/ZStacks/Crop/Row\_4/72/Holtz\_asty3\_I\_0276.jpg” “[1.03s]”  
[DEBUG][Qt] 01.11.2023 13:50:16 (unknown:0) - Switch to module: “SegmentEditor”  
[WARNING][Qt] 01.11.2023 13:50:16 (unknown:0) - QLayout::addChildLayout: layout “” already has a parent  
[DEBUG][Qt] 01.11.2023 13:50:30 (unknown:0) - Switch to module: “Volumes”  
[WARNING][Qt] 01.11.2023 13:50:30 (unknown:0) - ctkDoubleRangeSlider::setSingleStep( 0.0001 ) is outside of valid bounds.  
[DEBUG][Qt] 01.11.2023 13:50:45 (unknown:0) - Switch to module: “SegmentEditor”  
[DEBUG][Qt] 01.11.2023 13:51:48 (unknown:0) - Switch to module: “Volumes”  
[DEBUG][Qt] 01.11.2023 13:51:57 (unknown:0) - Switch to module: “SegmentEditor”  
[DEBUG][Qt] 01.11.2023 13:52:17 (unknown:0) - Switch to module: “Volumes”  
[DEBUG][Qt] 01.11.2023 13:52:29 (unknown:0) - Switch to module: “SegmentEditor”  
[DEBUG][Qt] 01.11.2023 14:06:03 (unknown:0) - Switch to module: “Volumes”  
[DEBUG][Qt] 01.11.2023 14:14:19 (unknown:0) - Switch to module: “SegmentEditor”

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Screenshot of the Issue ~\>

 ![Screenshot (1)](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/f/0f9ed7a7eb24eb2c34156b02c5bfb502276bef83.png)

Screenshot of Typical Behavior ~\>

 ![Screenshot (2)](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/2/b2fba4261c7e4a16097a2e3fbdf2fac2915bf733.jpeg)

NOTE: I replicated what the draw tool should look like by making the image spacing 1 mm.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [November 1, 2023, 8:16pm UTC](https://discourse.slicer.org/t/3d-slicer-paint-draw-tool-issue/32531/2 "2023-11-01T20:16:08Z")

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Segmentation geometry (origin, spacing, axis directions, and extents) is determined [from the geometry of the image that is selected first](https://slicer.readthedocs.io/en/latest/user_guide/modules/segmenteditor.html#cannot-paint-outside-some-boundaries). If you select a different image or change the image spacing, etc. then it will not affect the already created segmentation retrospectively. I would recommend to delete the segmentation and create a new one. That will be based on the new/updated image.

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**Author:** ![Cameron\_Shepherd](https://avatars.discourse-cdn.com/v4/letter/c/65b543/32.png) [@Cameron\_Shepherd](https://discourse.slicer.org/u/Cameron_Shepherd)\
**Post date:** [November 3, 2023, 12:08pm UTC](https://discourse.slicer.org/t/3d-slicer-paint-draw-tool-issue/32531/3 "2023-11-03T12:08:36Z")

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Thank you for your response. It appears that has fixed the problem I was having.