# Support **URL:** https://discourse.slicer.org/c/support/11.md?page=9 [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) **Page:** 10 --- ## [Surface Toolbox Clean model does not remove unconnected points](https://discourse.slicer.org/t/surface-toolbox-clean-model-does-not-remove-unconnected-points/46873)
**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\ **Replies:** 0\ **Last updated:** [April 29, 2026, 8:44pm UTC](https://discourse.slicer.org/t/surface-toolbox-clean-model-does-not-remove-unconnected-points/46873 "2026-04-29T20:44:10Z")
I have a model which has points which are not part of any triangles. When I use vtkImplicitPolyDataDistance filters, distances to these points can come back as always negative, which is supposed to indicate that the pro… --- ## [Question on Contour Editing](https://discourse.slicer.org/t/question-on-contour-editing/38230)
**Author:** [@alientex](https://discourse.slicer.org/u/alientex)\ **Replies:** 19\ **Last updated:** [April 29, 2026, 7:29pm UTC](https://discourse.slicer.org/t/question-on-contour-editing/38230 "2026-04-29T19:29:12Z")
Hello, Once a contour is available, I would like to manually adjust it by grabbing and moving the contour points. Additionally, a magnetic effect should be there to pull the constructed contour closer to the surface. I… --- ## [MONAI 3DSeg - Brain Glioma segmentation error](https://discourse.slicer.org/t/monai-3dseg-brain-glioma-segmentation-error/46870)
**Author:** [@Samim\_Zaheer](https://discourse.slicer.org/u/Samim_Zaheer)\ **Replies:** 1\ **Last updated:** [April 29, 2026, 5:09pm UTC](https://discourse.slicer.org/t/monai-3dseg-brain-glioma-segmentation-error/46870 "2026-04-29T17:09:05Z")
Operating system: macOS Slicer version: 5.10.0 Expected behavior: Glioma Segmentation Actual behavior: RuntimeError: affine matrix of all images should be the same for channel-wise concatenation. --- ## [Slicer 5.10 crashes when Ctrl + click-and-drag adjusts segment opacity](https://discourse.slicer.org/t/slicer-5-10-crashes-when-ctrl-click-and-drag-adjusts-segment-opacity/46719)
**Author:** [@MaxVs](https://discourse.slicer.org/u/MaxVs)\ **Replies:** 8\ **Last updated:** [April 28, 2026, 8:09pm UTC](https://discourse.slicer.org/t/slicer-5-10-crashes-when-ctrl-click-and-drag-adjusts-segment-opacity/46719 "2026-04-28T20:09:01Z")
Hi, I’ve encountered couple of crashes in a last few weeks. Everything works fine, and then the whole application closes up. It usually happnes when I change the opacity of the whole segmentation by holding left ctrl and… --- ## [I want to create a closed contour from hdr/img data](https://discourse.slicer.org/t/i-want-to-create-a-closed-contour-from-hdr-img-data/46860)
**Author:** [@PetrKryslUCSD](https://discourse.slicer.org/u/PetrKryslUCSD)\ **Replies:** 1\ **Last updated:** [April 28, 2026, 4:08pm UTC](https://discourse.slicer.org/t/i-want-to-create-a-closed-contour-from-hdr-img-data/46860 "2026-04-28T16:08:42Z")
Right now the contour runs into the boundary of the box, and it is then open. One thing that I could think of was to either surround the current volume with a layer of zero voxels (which would close the contour), or modi… --- ## [Is it possible to use Slicer to directly edit a 3D voxel volume?](https://discourse.slicer.org/t/is-it-possible-to-use-slicer-to-directly-edit-a-3d-voxel-volume/46859)
**Author:** [@PetrKryslUCSD](https://discourse.slicer.org/u/PetrKryslUCSD)\ **Replies:** 1\ **Last updated:** [April 28, 2026, 4:06pm UTC](https://discourse.slicer.org/t/is-it-possible-to-use-slicer-to-directly-edit-a-3d-voxel-volume/46859 "2026-04-28T16:06:24Z")
Has this been already solved or at least discussed? Such as inserting “voxelized” primitives (sphere, cylinder, block, …) and combining them in various ways (boolean ops?). --- ## [SlicerHeart and 2D echo](https://discourse.slicer.org/t/slicerheart-and-2d-echo/39844)
**Author:** [@Chuns\_SS](https://discourse.slicer.org/u/Chuns_SS)\ **Replies:** 1\ **Last updated:** [April 28, 2026, 12:03am UTC](https://discourse.slicer.org/t/slicerheart-and-2d-echo/39844 "2026-04-28T00:03:02Z")
I have a series of 99 dicom images of a echocardiogram but am having issue getiing anything to work in slicer heart module. all files start with 1: US ECHO 2D MM SPEC COL QUANT-EC \[01-99\] --- ## [Volume Property json file is incorrectly saved](https://discourse.slicer.org/t/volume-property-json-file-is-incorrectly-saved/46834)
**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\ **Replies:** 1\ **Last updated:** [April 27, 2026, 10:07pm UTC](https://discourse.slicer.org/t/volume-property-json-file-is-incorrectly-saved/46834 "2026-04-27T22:07:15Z")
I Load a 16bit unsigned dataset, set up its volume rendering properties such as Use shift slider Change the material preset to a non-default one (the second brightest) Remove some points from the scalar mapping and shi… --- ## [SlicerJupyter not available for latest version?](https://discourse.slicer.org/t/slicerjupyter-not-available-for-latest-version/41791)
**Author:** [@Juergen](https://discourse.slicer.org/u/Juergen)\ **Replies:** 11\ **Last updated:** [April 27, 2026, 2:41pm UTC](https://discourse.slicer.org/t/slicerjupyter-not-available-for-latest-version/41791 "2026-04-27T14:41:57Z")
Hello, I just noticed that SlicerJupyter was not available as an extension for both the latest stable version and the latest unstable version. What are the plans moving forward? Will SlicerJupyter work? SlicerJupyter i… --- ## [Tractography and anatomical research](https://discourse.slicer.org/t/tractography-and-anatomical-research/46805)
**Author:** [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)\ **Replies:** 3\ **Last updated:** [April 27, 2026, 9:27am UTC](https://discourse.slicer.org/t/tractography-and-anatomical-research/46805 "2026-04-27T09:27:46Z")
Hi, I wonder whether the algorithms used for tractography could be helpful to follow the path of muscle fibres through serial histologic sections --- ## [Need advice on Segmentation of CT scanned fossil specimen (lungfish)](https://discourse.slicer.org/t/need-advice-on-segmentation-of-ct-scanned-fossil-specimen-lungfish/46817)
**Author:** [@sturiones](https://discourse.slicer.org/u/sturiones)\ **Replies:** 5\ **Last updated:** [April 24, 2026, 9:21pm UTC](https://discourse.slicer.org/t/need-advice-on-segmentation-of-ct-scanned-fossil-specimen-lungfish/46817 "2026-04-24T21:21:42Z")
Hi, folks! I am not an expert in 3D Slicer, I need advice from the community. I have a TM-scanned fossil fish skull with inner structures (canals for nerves and vessels) of rather low contrast (the slice below is after … --- ## [Extensions-Manager: Extensions can not be installed](https://discourse.slicer.org/t/extensions-manager-extensions-can-not-be-installed/46824)
**Author:** [@juliangallaun](https://discourse.slicer.org/u/juliangallaun)\ **Replies:** 2\ **Last updated:** [April 24, 2026, 1:29pm UTC](https://discourse.slicer.org/t/extensions-manager-extensions-can-not-be-installed/46824 "2026-04-24T13:29:09Z")
Hello, I am unable to install new Extensions. Following message show up. Extensions can not be installed. Failed to load extension page using this URL: @KitwareMedical/slicer-extensions-webapp Check that 3D Slicer is… --- ## [Non-orthogonal IJK to RAS Direction Matrix](https://discourse.slicer.org/t/non-orthogonal-ijk-to-ras-direction-matrix/44644)
**Author:** [@mwirtz](https://discourse.slicer.org/u/mwirtz)\ **Replies:** 8\ **Last updated:** [April 24, 2026, 12:58pm UTC](https://discourse.slicer.org/t/non-orthogonal-ijk-to-ras-direction-matrix/44644 "2026-04-24T12:58:57Z")
Hey there! I am trying to load CT scans via the DICOM module, which have a non-zero GantryDetectorTilt (not 100% sure it is related) and it seems to cause a non-orthogonal IJK to RAS matrix (see screenshot). Also the ca… --- ## [TotalSegmentator keeps returning non-zero exit status 1](https://discourse.slicer.org/t/totalsegmentator-keeps-returning-non-zero-exit-status-1/46820)
**Author:** [@its-charliem](https://discourse.slicer.org/u/its-charliem)\ **Replies:** 0\ **Last updated:** [April 24, 2026, 1:24am UTC](https://discourse.slicer.org/t/totalsegmentator-keeps-returning-non-zero-exit-status-1/46820 "2026-04-24T01:24:49Z")
Problem report for 3D Slicer 5.10.0 win-amd64: \[please describe expected and actual behavior\] Command ‘\[‘C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../bin\\\\PythonSlicer.EXE’, ‘-m’, ‘pip’, ‘install’… --- ## [CTA vessel segmentation: petrous ICA vs bone overlap problem](https://discourse.slicer.org/t/cta-vessel-segmentation-petrous-ica-vs-bone-overlap-problem/46803)
**Author:** [@sandcastle](https://discourse.slicer.org/u/sandcastle)\ **Replies:** 2\ **Last updated:** [April 22, 2026, 7:26pm UTC](https://discourse.slicer.org/t/cta-vessel-segmentation-petrous-ica-vs-bone-overlap-problem/46803 "2026-04-22T19:26:03Z")
Hi all, I’ve been working on segmenting the circle of Willis and proximal carotids from CTA data. This has been straightforward with 3DRA and TOF-MRA, but I’m running into difficulty with the petrous ICA being inseparab… --- ## [DICOM 2D cine MRI is imported as Scalar Volume](https://discourse.slicer.org/t/dicom-2d-cine-mri-is-imported-as-scalar-volume/46792)
**Author:** [@aabrown100-git](https://discourse.slicer.org/u/aabrown100-git)\ **Replies:** 13\ **Last updated:** [April 22, 2026, 5:45am UTC](https://discourse.slicer.org/t/dicom-2d-cine-mri-is-imported-as-scalar-volume/46792 "2026-04-22T05:45:55Z")
I have a DICOM file containing a cine MRI on a single slice of the heart (4-chamber slice). I want this to load as a Sequence. Instead, it is loaded as a scalar volume, so that each time frame is treated as a different z… --- ## [Fiducial Registration Wizard transforms](https://discourse.slicer.org/t/fiducial-registration-wizard-transforms/46770)
**Author:** [@Zaky\_Alfarizi](https://discourse.slicer.org/u/Zaky_Alfarizi)\ **Replies:** 4\ **Last updated:** [April 20, 2026, 9:59am UTC](https://discourse.slicer.org/t/fiducial-registration-wizard-transforms/46770 "2026-04-20T09:59:06Z")
I’m a beginner, I already have a calibrated pointer. I have a tracker at my object in real life, the pointer should be relative to the tracker on my real life object/reference, right? So my pointer transform will be calc… --- ## [Converting .vtk to .inp file](https://discourse.slicer.org/t/converting-vtk-to-inp-file/46775)
**Author:** [@Tom\_F-T](https://discourse.slicer.org/u/Tom_F-T)\ **Replies:** 8\ **Last updated:** [April 18, 2026, 5:48pm UTC](https://discourse.slicer.org/t/converting-vtk-to-inp-file/46775 "2026-04-18T17:48:54Z")
I am trying to make a 3D model of trabecular bone for FEA in Abaqus. I am using slicer to convert the DICOM files of the bone into a 3D model, but when i first did this the .stl file i exported from slicer was only a sur… --- ## [Multiple Segments into 1 3D print](https://discourse.slicer.org/t/multiple-segments-into-1-3d-print/46771)
**Author:** [@Riley\_Maurath](https://discourse.slicer.org/u/Riley_Maurath)\ **Replies:** 1\ **Last updated:** [April 18, 2026, 12:11am UTC](https://discourse.slicer.org/t/multiple-segments-into-1-3d-print/46771 "2026-04-18T00:11:25Z")
I currently have 3 segments created in the 3D slicer and I am wanting to export them to be 3D printed. The issue I am running into are that the models are inside of each other and I am wanting to print them inside of eac… --- ## [New feature: Thick slab reconstruction from slice controllers and views](https://discourse.slicer.org/t/new-feature-thick-slab-reconstruction-from-slice-controllers-and-views/32432)
**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\ **Replies:** 12\ **Last updated:** [April 17, 2026, 11:18pm UTC](https://discourse.slicer.org/t/new-feature-thick-slab-reconstruction-from-slice-controllers-and-views/32432 "2026-04-17T23:18:51Z")
Thick slab reconstruction (TSR) can now be enabled and modified from the slice controllers and slice views! Enabling thick slab reconstruction as well as selection of the composite method (min, max, mean or sum) has bee… --- ## [Train AI for landmark detection](https://discourse.slicer.org/t/train-ai-for-landmark-detection/46734)
**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\ **Replies:** 6\ **Last updated:** [April 17, 2026, 6:16pm UTC](https://discourse.slicer.org/t/train-ai-for-landmark-detection/46734 "2026-04-17T18:16:18Z")
Hi, I’d like to ask here which are community suggestions about selecting an AI model and setting up training data for a medical landmark detection task. In my use case, I need to detect the superior tip of healthy kidn… --- ## [Exporting segmentation to Abaqus](https://discourse.slicer.org/t/exporting-segmentation-to-abaqus/13974)
**Author:** [@Jeff\_S](https://discourse.slicer.org/u/Jeff_S)\ **Replies:** 13\ **Last updated:** [April 17, 2026, 2:29pm UTC](https://discourse.slicer.org/t/exporting-segmentation-to-abaqus/13974 "2026-04-17T14:29:17Z")
Dear Andras, as I had troubles with FEBio, I am trying now to use the segmentation of the vertebra (in vtk format) to load into ABAQUS and do the simulation with that program. But it seems, that ABAQUS does not support … --- ## [TotalSegmentator Error on CT](https://discourse.slicer.org/t/totalsegmentator-error-on-ct/46757)
**Author:** [@ranahashemi](https://discourse.slicer.org/u/ranahashemi)\ **Replies:** 1\ **Last updated:** [April 16, 2026, 4:44pm UTC](https://discourse.slicer.org/t/totalsegmentator-error-on-ct/46757 "2026-04-16T16:44:46Z")
Hi everyone, I am using TotalSegmentator for a bone segmentation on CT scan DICOM files which I extracted from Ga68-PSMA PET/CT of our patients, the problem is the extension is working with some patients and then with th… --- ## [Change default destination folder in Export to files from segmentations module with python](https://discourse.slicer.org/t/change-default-destination-folder-in-export-to-files-from-segmentations-module-with-python/34697)
**Author:** [@garridojuan](https://discourse.slicer.org/u/garridojuan)\ **Replies:** 1\ **Last updated:** [April 16, 2026, 10:18am UTC](https://discourse.slicer.org/t/change-default-destination-folder-in-export-to-files-from-segmentations-module-with-python/34697 "2026-04-16T10:18:09Z")
I am developing a tool that automatically opens a segmentation mask and the image in 3D Slicer so that the user can modify it. I do it by using --python-code option when executing slicer from terminal. I would love to h… --- ## [slicer runs out of memory with large file.](https://discourse.slicer.org/t/slicer-runs-out-of-memory-with-large-file/46720)
**Author:** [@mhsheikh25](https://discourse.slicer.org/u/mhsheikh25)\ **Replies:** 5\ **Last updated:** [April 15, 2026, 6:31pm UTC](https://discourse.slicer.org/t/slicer-runs-out-of-memory-with-large-file/46720 "2026-04-15T18:31:02Z")
I have a Dell running 2 Platinum 8160 Xeons and 720GB ecc memory with a Nvidia 3090 24 GB video card and 3D slicer crashes on a large file with 300 Gb of memory remaining - error says that there isn’t enough memory. Is t… --- ## [ATLAS - BUILDER producing inverted template meshes?](https://discourse.slicer.org/t/atlas-builder-producing-inverted-template-meshes/46747)
**Author:** [@raranda22](https://discourse.slicer.org/u/raranda22)\ **Replies:** 2\ **Last updated:** [April 15, 2026, 3:59pm UTC](https://discourse.slicer.org/t/atlas-builder-producing-inverted-template-meshes/46747 "2026-04-15T15:59:12Z")
Hello, I’ve been attempting to make a template mesh via the BUILDER module of ATLAS. I’ve made several of these with different datasets, but this time it appears the template mesh produced is “inverted”. As you can see,… --- ## [Extracting STL from DICOM images to generate Brain Arteries geometry](https://discourse.slicer.org/t/extracting-stl-from-dicom-images-to-generate-brain-arteries-geometry/25215)
**Author:** [@Behzad\_Vahedi](https://discourse.slicer.org/u/Behzad_Vahedi)\ **Replies:** 13\ **Last updated:** [April 15, 2026, 11:16am UTC](https://discourse.slicer.org/t/extracting-stl-from-dicom-images-to-generate-brain-arteries-geometry/25215 "2026-04-15T11:16:47Z")
Hi My project is about computational fluid dynamic modeling of blood flow in an intracranial aneurysms. Can I extract the geometry from CT/Angio DICOM images in STL format in 3D Slicer? And if the answer is yes, is the… --- ## [Thick slab reconstruction and maximum/minimum intensity volume projections](https://discourse.slicer.org/t/thick-slab-reconstruction-and-maximum-minimum-intensity-volume-projections/34974)
**Author:** [@ddii](https://discourse.slicer.org/u/ddii)\ **Replies:** 2\ **Last updated:** [April 15, 2026, 3:23am UTC](https://discourse.slicer.org/t/thick-slab-reconstruction-and-maximum-minimum-intensity-volume-projections/34974 "2026-04-15T03:23:35Z")
How do you change the slice thickness? Thick slab reconstruction and maximum/minimum intensity volume projections This way does not work anymore… --- ## [2D MIP (maximum intensity projection) not works in Slicer 5.6.1](https://discourse.slicer.org/t/2d-mip-maximum-intensity-projection-not-works-in-slicer-5-6-1/36272)
**Author:** [@park](https://discourse.slicer.org/u/park)\ **Replies:** 4\ **Last updated:** [April 15, 2026, 3:20am UTC](https://discourse.slicer.org/t/2d-mip-maximum-intensity-projection-not-works-in-slicer-5-6-1/36272 "2026-04-15T03:20:29Z")
Hi all, I would like to make maximum intensity projection (MIP) in 2D view Thus, I tried the code below from the ‘script repository’ sliceNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSliceNodeRed") appLogic = slicer.ap… --- ## [Probe 3D Model in Slicer](https://discourse.slicer.org/t/probe-3d-model-in-slicer/31084)
**Author:** [@deringur](https://discourse.slicer.org/u/deringur)\ **Replies:** 17\ **Last updated:** [April 13, 2026, 8:56pm UTC](https://discourse.slicer.org/t/probe-3d-model-in-slicer/31084 "2026-04-13T20:56:18Z")
I am currently setting up a probe with the Motive software and OptiTrack camera system, and am transferring the live location data to Slicer via PLUS. Is there way to create a 3D model for the probe to view on Slicer (cl… [Previous page](https://discourse.slicer.org/c/support/11.md?page=8) [Next page](https://discourse.slicer.org/c/support/11.md?page=10)