# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=29

[Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md)

**Page:** 30

---

## [Help with Transform Inversion and Modifying PLUS Transformation in Slicer](https://discourse.slicer.org/t/help-with-transform-inversion-and-modifying-plus-transformation-in-slicer/44284)

<div class="topic-metadata">

**Author:** [@daimon2](https://discourse.slicer.org/u/daimon2)\
**Replies:** 2\
**Last updated:** [August 31, 2025, 7:41pm UTC](https://discourse.slicer.org/t/help-with-transform-inversion-and-modifying-plus-transformation-in-slicer/44284 "2025-08-31T19:41:18Z")

</div>

Dear Slicer Community, I am a beginner working through the tutorial “day2\_PrototypingImageGuidedTherapyApplications,” and I need some help with transformations. The transformation I am receiving from Optitrack through P…

---

## [How stl. to alignment accurately?](https://discourse.slicer.org/t/how-stl-to-alignment-accurately/44294)

<div class="topic-metadata">

**Author:** [@guozhuang](https://discourse.slicer.org/u/guozhuang)\
**Replies:** 0\
**Last updated:** [August 31, 2025, 7:35pm UTC](https://discourse.slicer.org/t/how-stl-to-alignment-accurately/44294 "2025-08-31T19:35:11Z")

</div>

I have two documents(stl.), I want to align them and try measure the location of implants, but I used FastModelAlign, it shows significant differences, I would like to know if there are any other registration methods ava…

---

## [How to import slicer transfoms (.h5 files) into Blender?](https://discourse.slicer.org/t/how-to-import-slicer-transfoms-h5-files-into-blender/44286)

<div class="topic-metadata">

**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\
**Replies:** 1\
**Last updated:** [August 31, 2025, 7:34pm UTC](https://discourse.slicer.org/t/how-to-import-slicer-transfoms-h5-files-into-blender/44286 "2025-08-31T19:34:59Z")

</div>

Hi everyone! I want to extract rotation and position data from an Slicer transform (TR.h5) into Blender. For now, I did: 1.- Install h5py library in Blender with add-on blender\_pip: Python module manager from GitHub -…

---

## [Neuronavigation using Kinect sensor](https://discourse.slicer.org/t/neuronavigation-using-kinect-sensor/44290)

<div class="topic-metadata">

**Author:** [@coldfire85](https://discourse.slicer.org/u/coldfire85)\
**Replies:** 0\
**Last updated:** [August 31, 2025, 11:24am UTC](https://discourse.slicer.org/t/neuronavigation-using-kinect-sensor/44290 "2025-08-31T11:24:44Z")

</div>

I am trying to implement Neuronavigation using Kinect Hardware , till now i have built the plus-server to recognise the Kinect hardware and i get both RGB and Depth streams and RGB-D (Fused streams) as well , I am wonder…

---

## [The values in the rotation field are not saved](https://discourse.slicer.org/t/the-values-in-the-rotation-field-are-not-saved/44234)

<div class="topic-metadata">

**Author:** [@Konstantin](https://discourse.slicer.org/u/Konstantin)\
**Replies:** 8\
**Last updated:** [August 30, 2025, 5:44am UTC](https://discourse.slicer.org/t/the-values-in-the-rotation-field-are-not-saved/44234 "2025-08-30T05:44:23Z")

</div>

Hello everyone. I have a task - to record the displacement of fragments in all planes when they move. I use the transforms module. But I encountered the following problem: all values ​​in the “rotation” field are reset t…

---

## [How to Convert .mhd + .raw 3D Time-Series Images into a 4D DICOM in 3D Slicer?](https://discourse.slicer.org/t/how-to-convert-mhd-raw-3d-time-series-images-into-a-4d-dicom-in-3d-slicer/44280)

<div class="topic-metadata">

**Author:** [@sprp2025uci](https://discourse.slicer.org/u/sprp2025uci)\
**Replies:** 1\
**Last updated:** [August 30, 2025, 4:12am UTC](https://discourse.slicer.org/t/how-to-convert-mhd-raw-3d-time-series-images-into-a-4d-dicom-in-3d-slicer/44280 "2025-08-30T04:12:02Z")

</div>

Hi, I am working with publicly available 3D echocardiographic datasets stored as .mhd + .raw files, along with corresponding .vtk mesh files for each time frame. I would like to convert these into a single 4D DICOM (cin…

---

## [Is branch splitting like VMTK tutorial possible in Slicer?](https://discourse.slicer.org/t/is-branch-splitting-like-vmtk-tutorial-possible-in-slicer/44273)

<div class="topic-metadata">

**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 2\
**Last updated:** [August 29, 2025, 10:21pm UTC](https://discourse.slicer.org/t/is-branch-splitting-like-vmtk-tutorial-possible-in-slicer/44273 "2025-08-29T22:21:30Z")

</div>

I am interested in carrying out branch splitting exactly as shown in this tutorial: Branch Splitting | vmtk - the Vascular Modelling Toolkit I am familiar with using vmtk for single centerlines, and am now exploring it…

---

## [Annoying frame after slice view on 3d](https://discourse.slicer.org/t/annoying-frame-after-slice-view-on-3d/44247)

<div class="topic-metadata">

**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 7\
**Last updated:** [August 29, 2025, 10:16pm UTC](https://discourse.slicer.org/t/annoying-frame-after-slice-view-on-3d/44247 "2025-08-29T22:16:34Z")

</div>

often i get this frame not going away after slice view on 3d . no matter what i do i cant get rid of . i have to start all over again

---

## [Resize and move the slice view interactively in the 3D view](https://discourse.slicer.org/t/resize-and-move-the-slice-view-interactively-in-the-3d-view/44270)

<div class="topic-metadata">

**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 0\
**Last updated:** [August 29, 2025, 6:30pm UTC](https://discourse.slicer.org/t/resize-and-move-the-slice-view-interactively-in-the-3d-view/44270 "2025-08-29T18:30:26Z")

</div>

is it possible to re size the slice being viewed on 3d ? i manipulate the size of the slice view and move the center around to adjust the size of slice . it would be great if that can be done natively

---

## [Radiomics feature extraction](https://discourse.slicer.org/t/radiomics-feature-extraction/44267)

<div class="topic-metadata">

**Author:** [@Meltem](https://discourse.slicer.org/u/Meltem)\
**Replies:** 1\
**Last updated:** [August 29, 2025, 6:44pm UTC](https://discourse.slicer.org/t/radiomics-feature-extraction/44267 "2025-08-29T18:44:26Z")

</div>

Hello. I am using 3D Slicer 5.8.1 for my radiomics study. I already have radiologic images (mri) in nifti format and segmentations in nrrd format. What should I do to extract features using my images and segmentations? I…

---

## [How to create dynamic StylusToReference transform from NDI tracker data?](https://discourse.slicer.org/t/how-to-create-dynamic-stylustoreference-transform-from-ndi-tracker-data/44254)

<div class="topic-metadata">

**Author:** [@jonh\_wick](https://discourse.slicer.org/u/jonh_wick)\
**Replies:** 1\
**Last updated:** [August 29, 2025, 6:28pm UTC](https://discourse.slicer.org/t/how-to-create-dynamic-stylustoreference-transform-from-ndi-tracker-data/44254 "2025-08-29T18:28:30Z")

</div>

Hi all,大家好 I am working with an NDI tracker in 3D Slicer and I have two transforms provided dynamically by the tracker: StylusToTracker ReferenceToTracker What I would like to obtain in real time is the transfo…

---

## [Can't open a local file on web UI?](https://discourse.slicer.org/t/cant-open-a-local-file-on-web-ui/44255)

<div class="topic-metadata">

**Author:** [@Rod\_Whiteley](https://discourse.slicer.org/u/Rod_Whiteley)\
**Replies:** 3\
**Last updated:** [August 29, 2025, 5:26pm UTC](https://discourse.slicer.org/t/cant-open-a-local-file-on-web-ui/44255 "2025-08-29T17:26:40Z")

</div>

Operating system: Windows 11 Slicer version: 5.03 Expected behavior: Upload a nrrd file to analyse Actual behavior: can’t access local files (Downloads folder) from

---

## [Surface Measurements & Model Comparison in 3D Slicer](https://discourse.slicer.org/t/surface-measurements-model-comparison-in-3d-slicer/44264)

<div class="topic-metadata">

**Author:** [@Faisal\_Alshaikh](https://discourse.slicer.org/u/Faisal_Alshaikh)\
**Replies:** 1\
**Last updated:** [August 29, 2025, 5:12pm UTC](https://discourse.slicer.org/t/surface-measurements-model-comparison-in-3d-slicer/44264 "2025-08-29T17:12:59Z")

</div>

Hello everyone, I am currently testing 3D Slicer with surface models exported from the Vectra H2 system (.obj format with texture). The models import and display correctly in the 3D view, but I could not find direct opt…

---

## [Slicer Crashing on MacOS Sequoia 15.6.1](https://discourse.slicer.org/t/slicer-crashing-on-macos-sequoia-15-6-1/44250)

<div class="topic-metadata">

**Author:** [@Joseph\_Pincus](https://discourse.slicer.org/u/Joseph_Pincus)\
**Replies:** 4\
**Last updated:** [August 29, 2025, 3:07pm UTC](https://discourse.slicer.org/t/slicer-crashing-on-macos-sequoia-15-6-1/44250 "2025-08-29T15:07:24Z")

</div>

Hi all, I am working on a relatively simple project taking some measurements on MRIs. I have an M3 processor running MacOS Sequoia 15.6.1 with 18GB of memory. I am running Slicer 5.8.1. It was working fine for months, …

---

## [How to manipulate a 4D ultrasound DICOM file](https://discourse.slicer.org/t/how-to-manipulate-a-4d-ultrasound-dicom-file/44258)

<div class="topic-metadata">

**Author:** [@francio](https://discourse.slicer.org/u/francio)\
**Replies:** 1\
**Last updated:** [August 29, 2025, 2:55pm UTC](https://discourse.slicer.org/t/how-to-manipulate-a-4d-ultrasound-dicom-file/44258 "2025-08-29T14:55:05Z")

</div>

Hello, im looking to manipulate a 4D torax ultrasound volume (3D + time) with 3D Slicer, i was wondering if there was any plug in necessary in order to do this. Also if anyone knows if it is possible to set coordinates f…

---

## [CBCTToothSegmentation failed to compute results error](https://discourse.slicer.org/t/cbcttoothsegmentation-failed-to-compute-results-error/44251)

<div class="topic-metadata">

**Author:** [@Philipp\_Frobel](https://discourse.slicer.org/u/Philipp_Frobel)\
**Replies:** 0\
**Last updated:** [August 29, 2025, 2:34pm UTC](https://discourse.slicer.org/t/cbcttoothsegmentation-failed-to-compute-results-error/44251 "2025-08-29T14:34:42Z")

</div>

Hi everyone, when i try to segmentate a tooth with the BCTToothSegmentation extention i always get the same error. Any ideas how to fix this or what i do wrong?

---

## [Check surface meshes generated with the surface toolbox](https://discourse.slicer.org/t/check-surface-meshes-generated-with-the-surface-toolbox/44207)

<div class="topic-metadata">

**Author:** [@DaSt](https://discourse.slicer.org/u/DaSt)\
**Replies:** 3\
**Last updated:** [August 29, 2025, 4:54am UTC](https://discourse.slicer.org/t/check-surface-meshes-generated-with-the-surface-toolbox/44207 "2025-08-29T04:54:41Z")

</div>

Dear All, I’m using the Surface Toolbox, specifically Uniform Remesh, via the Python API to generate STL surface meshes with a target edge length. Occasionally the resulting STL is not watertight (e.g., open boundaries …

---

## [Add keyboard and mouse shortcuts for Module Selector navigation](https://discourse.slicer.org/t/add-keyboard-and-mouse-shortcuts-for-module-selector-navigation/44235)

<div class="topic-metadata">

**Author:** [@ruffsl](https://discourse.slicer.org/u/ruffsl)\
**Replies:** 0\
**Last updated:** [August 28, 2025, 7:34pm UTC](https://discourse.slicer.org/t/add-keyboard-and-mouse-shortcuts-for-module-selector-navigation/44235 "2025-08-28T19:34:04Z")

</div>

---

## [Head oculomotor task in total segmentator nor working](https://discourse.slicer.org/t/head-oculomotor-task-in-total-segmentator-nor-working/44158)

<div class="topic-metadata">

**Author:** [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)\
**Replies:** 1\
**Last updated:** [August 27, 2025, 1:59pm UTC](https://discourse.slicer.org/t/head-oculomotor-task-in-total-segmentator-nor-working/44158 "2025-08-27T13:59:25Z")

</div>

I can’t operate total segmentator with the task oculomotor muscles, I got an error message when making any attempt. I am running Slicer 5,9,0 25-08-14 on a Mac Apple chip M2 Sequoia 15.6. What is wrong? Here after t…

---

## [Error using Elastix registration: returned non-zero exit status 1](https://discourse.slicer.org/t/error-using-elastix-registration-returned-non-zero-exit-status-1/30140)

<div class="topic-metadata">

**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 1\
**Last updated:** [August 27, 2025, 2:39am UTC](https://discourse.slicer.org/t/error-using-elastix-registration-returned-non-zero-exit-status-1/30140 "2025-08-27T02:39:44Z")

</div>

Hi to everyone :slight\_smile: On this occasion we are struggling with registration with Elastix module. The goal is registrate two CT images with the next workflow: Load the images as Slicer´s volumes. Open the El…

---

## [Issue with eraser function](https://discourse.slicer.org/t/issue-with-eraser-function/43825)

<div class="topic-metadata">

**Author:** [@noi9](https://discourse.slicer.org/u/noi9)\
**Replies:** 5\
**Last updated:** [August 26, 2025, 2:33pm UTC](https://discourse.slicer.org/t/issue-with-eraser-function/43825 "2025-08-26T14:33:28Z")

</div>

Hi, Two issues which may be related. When I used the eraser function, there is still faint markings left. It does not fully erase. There appears to be artefact when I used the threshold button to fill out multipl…

---

## [Slice-indicator lines in orthogonal views?](https://discourse.slicer.org/t/slice-indicator-lines-in-orthogonal-views/42233)

<div class="topic-metadata">

**Author:** [@robertf](https://discourse.slicer.org/u/robertf)\
**Replies:** 5\
**Last updated:** [August 26, 2025, 10:26am UTC](https://discourse.slicer.org/t/slice-indicator-lines-in-orthogonal-views/42233 "2025-08-26T10:26:58Z")

</div>

When displaying orthogonal views, I would like to have lines displayed in each view that indicate the positions of the slices viewed in the other two views? For example, in the image below, red and yellow lines are shown…

---

## [Extension Manager crash](https://discourse.slicer.org/t/extension-manager-crash/44199)

<div class="topic-metadata">

**Author:** [@Catalina\_Balzo](https://discourse.slicer.org/u/Catalina_Balzo)\
**Replies:** 3\
**Last updated:** [August 26, 2025, 10:01am UTC](https://discourse.slicer.org/t/extension-manager-crash/44199 "2025-08-26T10:01:31Z")

</div>

Hi, I recently tried to upgrade my slicer from version 5.6 to 5.8.1, but I encountered a serious problem. Version 5.8.1 runs fine, but whenever I try to open the Extension Manager the program crashes. Because of this, I …

---

## [Dental segmentator output editing](https://discourse.slicer.org/t/dental-segmentator-output-editing/44144)

<div class="topic-metadata">

**Author:** [@scarlet](https://discourse.slicer.org/u/scarlet)\
**Replies:** 2\
**Last updated:** [August 26, 2025, 6:47am UTC](https://discourse.slicer.org/t/dental-segmentator-output-editing/44144 "2025-08-26T06:47:02Z")

</div>

When I use dental segmentator module on CBCT, some gaps are still left inside the jaw bones. What is the easiest way to fill in that empty space.

---

## [Removing below threshold data from segment](https://discourse.slicer.org/t/removing-below-threshold-data-from-segment/44184)

<div class="topic-metadata">

**Author:** [@Learn34](https://discourse.slicer.org/u/Learn34)\
**Replies:** 3\
**Last updated:** [August 25, 2025, 2:23pm UTC](https://discourse.slicer.org/t/removing-below-threshold-data-from-segment/44184 "2025-08-25T14:23:50Z")

</div>

Big picture: I want to convert the CT scan data from a SPECT of my spine into a finite element model to validate use of a novel implant in a repair thereof. Little picture: In attempting to follow this workflow for conv…

---

## [Animal automatic segmentation](https://discourse.slicer.org/t/animal-automatic-segmentation/44182)

<div class="topic-metadata">

**Author:** [@Melodicpinpon](https://discourse.slicer.org/u/Melodicpinpon)\
**Replies:** 2\
**Last updated:** [August 24, 2025, 6:40pm UTC](https://discourse.slicer.org/t/animal-automatic-segmentation/44182 "2025-08-24T18:40:45Z")

</div>

Hi everyone, As the tools for automatic segmentation are evolving rapidly, Is there any similar tool meant for animals (dogs or cats?). I’ve tried Total Segmentator on a dog CTscan and on a pig and it kind of work but …

---

## [Saving a trained MONAILabel model.](https://discourse.slicer.org/t/saving-a-trained-monailabel-model/44186)

<div class="topic-metadata">

**Author:** [@okkar\_kyaw](https://discourse.slicer.org/u/okkar_kyaw)\
**Replies:** 0\
**Last updated:** [August 24, 2025, 1:21am UTC](https://discourse.slicer.org/t/saving-a-trained-monailabel-model/44186 "2025-08-24T01:21:40Z")

</div>

After annotations and and training the model. How do I save my already trained .pt file for later use and sharing between researcher ? Is there a buttom to do this?

---

## [OBB Corner Coordinates and/or Dimensions](https://discourse.slicer.org/t/obb-corner-coordinates-and-or-dimensions/44176)

<div class="topic-metadata">

**Author:** [@liam26](https://discourse.slicer.org/u/liam26)\
**Replies:** 3\
**Last updated:** [August 23, 2025, 11:19pm UTC](https://discourse.slicer.org/t/obb-corner-coordinates-and-or-dimensions/44176 "2025-08-23T23:19:11Z")

</div>

I’m trying to find the dimensions of my OBB box (width, length, height) to get the height of spinal discs. Even getting the corner coordinates would be helpful so I could calculate it manually. I can’t find an existing s…

---

## [Potential JAX-based physics for real-time simulation in Slicer?](https://discourse.slicer.org/t/potential-jax-based-physics-for-real-time-simulation-in-slicer/44142)

<div class="topic-metadata">

**Author:** [@Bruce\_Hu](https://discourse.slicer.org/u/Bruce_Hu)\
**Replies:** 6\
**Last updated:** [August 23, 2025, 7:58pm UTC](https://discourse.slicer.org/t/potential-jax-based-physics-for-real-time-simulation-in-slicer/44142 "2025-08-23T19:58:45Z")

</div>

Hello Slicer community, I’m a developer interested in physics simulation. My project, brax viewer, visualizes JAX-based physics engines in real time, which is a new open-source package developed as part of Google Summer…

---

## [Create STL RT Structures with MRI  to DICOM RT Strcutures](https://discourse.slicer.org/t/create-stl-rt-structures-with-mri-to-dicom-rt-strcutures/44104)

<div class="topic-metadata">

**Author:** [@ar24](https://discourse.slicer.org/u/ar24)\
**Replies:** 1\
**Last updated:** [August 22, 2025, 9:41am UTC](https://discourse.slicer.org/t/create-stl-rt-structures-with-mri-to-dicom-rt-strcutures/44104 "2025-08-22T09:41:23Z")

</div>

I like to see if I can use 3D slicer to convert STL RT file format on MRI to Dicom File Format for Treatment planning

[Previous page](https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=28)

[Next page](https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=30)