# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=106

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

**Page:** 107

---

## [Using slicer as a Jupyter kernel, how to set up a variable inspector](https://discourse.slicer.org/t/using-slicer-as-a-jupyter-kernel-how-to-set-up-a-variable-inspector/35054)

<div class="topic-metadata">

**Author:** [@Matteboo](https://discourse.slicer.org/u/Matteboo)\
**Replies:** 0\
**Last updated:** [March 25, 2024, 1:51pm UTC](https://discourse.slicer.org/t/using-slicer-as-a-jupyter-kernel-how-to-set-up-a-variable-inspector/35054 "2024-03-25T13:51:43Z")

</div>

Hello, I recently started to use Slicer as a Jupyter kernel. I’m setting up the environment and I’m trying to set up a variable inspector. I installed this extension however, it’s not working. When I launch a noteb…

---

## [How can I record multiple video inputs at the same time from Slicer?](https://discourse.slicer.org/t/how-can-i-record-multiple-video-inputs-at-the-same-time-from-slicer/20928)

<div class="topic-metadata">

**Author:** [@lb123](https://discourse.slicer.org/u/lb123)\
**Replies:** 16\
**Last updated:** [March 25, 2024, 11:59am UTC](https://discourse.slicer.org/t/how-can-i-record-multiple-video-inputs-at-the-same-time-from-slicer/20928 "2024-03-25T11:59:54Z")

</div>

Hi, I’m broadcasting 2 acquired videos through OpenIGTLink from Plus Server to Slicer 4.13.0. The videos consist in live data coming from 2 epiphan frame grabbers. I can correctly see both the live videos on Slicer. I…

---

## [Change letter size in interface messages](https://discourse.slicer.org/t/change-letter-size-in-interface-messages/35023)

<div class="topic-metadata">

**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 2\
**Last updated:** [March 25, 2024, 9:36am UTC](https://discourse.slicer.org/t/change-letter-size-in-interface-messages/35023 "2024-03-25T09:36:30Z")

</div>

Hi to everyone. Today I’m interested in interface configuration. At this moment, the way I use to communicate info to the users is displaying text in the lower left corner using: slicer.util.showStatusMessage("Editing …

---

## [Slicer Docker for GUI via browser](https://discourse.slicer.org/t/slicer-docker-for-gui-via-browser/22539)

<div class="topic-metadata">

**Author:** [@Nadya\_Shusharina](https://discourse.slicer.org/u/Nadya_Shusharina)\
**Replies:** 10\
**Last updated:** [March 24, 2024, 12:27pm UTC](https://discourse.slicer.org/t/slicer-docker-for-gui-via-browser/22539 "2024-03-24T12:27:31Z")

</div>

I would like to use a web browser to access the Slicer GUI for a slicer instance running in a docker container. SlicerDocker/slicer-notebook includes a Dockerfile to expose a Jupyter notebook attached to the slicer kern…

---

## [Automate camera translation (zoom into volume) into a sequence](https://discourse.slicer.org/t/automate-camera-translation-zoom-into-volume-into-a-sequence/35028)

<div class="topic-metadata">

**Author:** [@AndrewWeitz](https://discourse.slicer.org/u/AndrewWeitz)\
**Replies:** 1\
**Last updated:** [March 22, 2024, 10:23pm UTC](https://discourse.slicer.org/t/automate-camera-translation-zoom-into-volume-into-a-sequence/35028 "2024-03-22T22:23:58Z")

</div>

Is there a way to vectorize the zoom in/out of the camera. i.e. camera starts at position (1,0,0) and then zooms into position (5,0,0). Looking to create an automated sequence that starts with the volume zoomed out and t…

---

## [Failed to detect end points: openSurfaceAtPoint failed: empty input polydata Error](https://discourse.slicer.org/t/failed-to-detect-end-points-opensurfaceatpoint-failed-empty-input-polydata-error/35029)

<div class="topic-metadata">

**Author:** [@sthaker](https://discourse.slicer.org/u/sthaker)\
**Replies:** 0\
**Last updated:** [March 22, 2024, 8:40pm UTC](https://discourse.slicer.org/t/failed-to-detect-end-points-opensurfaceatpoint-failed-empty-input-polydata-error/35029 "2024-03-22T20:40:29Z")

</div>

Hello, I am uploading stl files of aortas as I normally do to extract centerlines using the “Extract Centerline” module. However, when I go to first set the endpoints, I get the error shown above. Nothing looks wrong wi…

---

## [Using DRRGeneratorModule in a Python script](https://discourse.slicer.org/t/using-drrgeneratormodule-in-a-python-script/35022)

<div class="topic-metadata">

**Author:** [@Yassin\_Abdelrahman](https://discourse.slicer.org/u/Yassin_Abdelrahman)\
**Replies:** 0\
**Last updated:** [March 22, 2024, 1:36pm UTC](https://discourse.slicer.org/t/using-drrgeneratormodule-in-a-python-script/35022 "2024-03-22T13:36:25Z")

</div>

Hi all, I would like to use the above module in a python script but am unsure how to do so. Below is something I have tried but I do not have that much experience in working in Slicer so I think I am misunderstanding th…

---

## [Deforming with NiftyReg is different than deforming in Slicer](https://discourse.slicer.org/t/deforming-with-niftyreg-is-different-than-deforming-in-slicer/34992)

<div class="topic-metadata">

**Author:** [@koeglfryderyk](https://discourse.slicer.org/u/koeglfryderyk)\
**Replies:** 3\
**Last updated:** [March 22, 2024, 1:23am UTC](https://discourse.slicer.org/t/deforming-with-niftyreg-is-different-than-deforming-in-slicer/34992 "2024-03-22T01:23:37Z")

</div>

I’m integrating NiftyReg into an extension. (one of the goals is to get the computed transformation/deformation into Slicer) I registered two images with reg\_f3d and saved the control point grid (to later get the deform…

---

## [Segmenting DICOM Images](https://discourse.slicer.org/t/segmenting-dicom-images/35008)

<div class="topic-metadata">

**Author:** [@Akhil](https://discourse.slicer.org/u/Akhil)\
**Replies:** 1\
**Last updated:** [March 22, 2024, 1:22am UTC](https://discourse.slicer.org/t/segmenting-dicom-images/35008 "2024-03-22T01:22:00Z")

</div>

I am new to 3D SLicer. My task is to segment a DICOM image of an Interested region. I am unable to find some useful resources also. Please give some insights on how to segment that. Currently, I can upload the DICOM file…

---

## [Helper app to manage slicer installations](https://discourse.slicer.org/t/helper-app-to-manage-slicer-installations/35007)

<div class="topic-metadata">

**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 0\
**Last updated:** [March 21, 2024, 3:00pm UTC](https://discourse.slicer.org/t/helper-app-to-manage-slicer-installations/35007 "2024-03-21T15:00:52Z")

</div>

Here’s an idea people may want to comment on:

---

## [Creating a volumetric mesh from a surface model](https://discourse.slicer.org/t/creating-a-volumetric-mesh-from-a-surface-model/34993)

<div class="topic-metadata">

**Author:** [@HBhramd](https://discourse.slicer.org/u/HBhramd)\
**Replies:** 0\
**Last updated:** [March 20, 2024, 7:45pm UTC](https://discourse.slicer.org/t/creating-a-volumetric-mesh-from-a-surface-model/34993 "2024-03-20T19:45:43Z")

</div>

I need to convert a surface model that was created in Blender into a solid, volumetric mesh. The original file is in .obj format. I also need to save the volumetric mesh as a format that can be read by R (for research pu…

---

## [3D Slicer linked to Blender](https://discourse.slicer.org/t/3d-slicer-linked-to-blender/29213)

<div class="topic-metadata">

**Author:** [@yun\_zou](https://discourse.slicer.org/u/yun_zou)\
**Replies:** 14\
**Last updated:** [March 20, 2024, 7:10pm UTC](https://discourse.slicer.org/t/3d-slicer-linked-to-blender/29213 "2024-03-20T19:10:38Z")

</div>

I want to know how to make 3dslicer and blender connect and interact in real time. For example: if I drag any view in 3dslicer, the three view planes in blender will also move accordingly. The model in blender can also b…

---

## [Irregular volume geometry detected when exporting DCM](https://discourse.slicer.org/t/irregular-volume-geometry-detected-when-exporting-dcm/34947)

<div class="topic-metadata">

**Author:** [@kkkkkkk123](https://discourse.slicer.org/u/kkkkkkk123)\
**Replies:** 2\
**Last updated:** [March 20, 2024, 8:15am UTC](https://discourse.slicer.org/t/irregular-volume-geometry-detected-when-exporting-dcm/34947 "2024-03-20T08:15:01Z")

</div>

Hello, I applied the Gaussian Blur Image Filter to a PET series and exported the result to DICOM. However, when I import the new series in the DICOM browser and load them into the Scene, an acquisition transform is gener…

---

## [Bug in island tool?](https://discourse.slicer.org/t/bug-in-island-tool/34987)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 0\
**Last updated:** [March 20, 2024, 3:43am UTC](https://discourse.slicer.org/t/bug-in-island-tool/34987 "2024-03-20T03:43:36Z")

</div>

At this stage, I want to remove small clusters within the Segment\_2. I set the editable area Inside Segment\_2 (red), set the small cluster size 100 voxels. When I run this, everything Segment\_2 is essentially cleared. Af…

---

## [Adding color property to fcsv files created in matlab](https://discourse.slicer.org/t/adding-color-property-to-fcsv-files-created-in-matlab/34984)

<div class="topic-metadata">

**Author:** [@FatihSogukpinar](https://discourse.slicer.org/u/FatihSogukpinar)\
**Replies:** 3\
**Last updated:** [March 19, 2024, 8:38pm UTC](https://discourse.slicer.org/t/adding-color-property-to-fcsv-files-created-in-matlab/34984 "2024-03-19T20:38:36Z")

</div>

Hi all, In Matlab, I have a function to create .fcsv files to visualize my recording sites in Slicer. Now, I want to be able to add color property to the each recording site. I cannot do this manually using Markups mod…

---

## [Help to Segment Multiple Sclerosis Plaques with MONAI Label](https://discourse.slicer.org/t/help-to-segment-multiple-sclerosis-plaques-with-monai-label/34983)

<div class="topic-metadata">

**Author:** [@franbuemi](https://discourse.slicer.org/u/franbuemi)\
**Replies:** 0\
**Last updated:** [March 19, 2024, 5:39pm UTC](https://discourse.slicer.org/t/help-to-segment-multiple-sclerosis-plaques-with-monai-label/34983 "2024-03-19T17:39:49Z")

</div>

Hi everyone, I would like to train a model to segment multiple sclerosis plaques on 3D FLAIR images, one by one, each with distinct labels. I’ve started with a dataset of 10 patients just to get started before tackling s…

---

## [Solid body vs. sheet body](https://discourse.slicer.org/t/solid-body-vs-sheet-body/34982)

<div class="topic-metadata">

**Author:** [@Marthe](https://discourse.slicer.org/u/Marthe)\
**Replies:** 1\
**Last updated:** [March 19, 2024, 5:33pm UTC](https://discourse.slicer.org/t/solid-body-vs-sheet-body/34982 "2024-03-19T17:33:35Z")

</div>

When I export an STL file of the ribcage I segmented from 3D Slicer CTACardio CT scan, I obtain a solid body in CAD software for further processing of the body. However, when I export an STL file of this ribcage after pe…

---

## [How to cut ultrasound image from interface](https://discourse.slicer.org/t/how-to-cut-ultrasound-image-from-interface/34979)

<div class="topic-metadata">

**Author:** [@LeidyMoraV](https://discourse.slicer.org/u/LeidyMoraV)\
**Replies:** 0\
**Last updated:** [March 19, 2024, 4:28pm UTC](https://discourse.slicer.org/t/how-to-cut-ultrasound-image-from-interface/34979 "2024-03-19T16:28:12Z")

</div>

Hi, I’m using volume reconstruction module, but the user interface is being reconstructed too, I want to only use the ultrasound image in itself, I’ve tried using ClipRectangleOrigin = "200 206" ClipRectangleSize = "532…

---

## [What's the difference between .zraw file and .raw file](https://discourse.slicer.org/t/whats-the-difference-between-zraw-file-and-raw-file/34971)

<div class="topic-metadata">

**Author:** [@Chuan](https://discourse.slicer.org/u/Chuan)\
**Replies:** 1\
**Last updated:** [March 19, 2024, 3:33pm UTC](https://discourse.slicer.org/t/whats-the-difference-between-zraw-file-and-raw-file/34971 "2024-03-19T15:33:47Z")

</div>

Hi all, Recently I meet a very strange problem when I save my data as mhd file. Sometimes it will save as a group of mhd file + raw file, which looks normal and correct. But sometimes it will save as a group of mhd fil…

---

## [Merging Connected Components](https://discourse.slicer.org/t/merging-connected-components/34975)

<div class="topic-metadata">

**Author:** [@rkraaijveld](https://discourse.slicer.org/u/rkraaijveld)\
**Replies:** 0\
**Last updated:** [March 19, 2024, 1:58pm UTC](https://discourse.slicer.org/t/merging-connected-components/34975 "2024-03-19T13:58:58Z")

</div>

Hi, I’d like to create a button in my extension that merges all the segmentations in the image. I found this: Slicer: vtkSegmentation Class Reference Where I see that I can use GenerateMergedLabelmap() and GenerateMer…

---

## [Can anyone tell where i can get dwi datatset for tumor patients?](https://discourse.slicer.org/t/can-anyone-tell-where-i-can-get-dwi-datatset-for-tumor-patients/34970)

<div class="topic-metadata">

**Author:** [@Pranali](https://discourse.slicer.org/u/Pranali)\
**Replies:** 0\
**Last updated:** [March 19, 2024, 8:42am UTC](https://discourse.slicer.org/t/can-anyone-tell-where-i-can-get-dwi-datatset-for-tumor-patients/34970 "2024-03-19T08:42:55Z")

</div>

I’m working on analyzing fiber tracts for tumor patients. But I want a dataset of DWI patients with tumors. can anyone tell where I can get it? Thank You

---

## [How to meaure a single field](https://discourse.slicer.org/t/how-to-meaure-a-single-field/34962)

<div class="topic-metadata">

**Author:** [@shir](https://discourse.slicer.org/u/shir)\
**Replies:** 1\
**Last updated:** [March 18, 2024, 7:48pm UTC](https://discourse.slicer.org/t/how-to-meaure-a-single-field/34962 "2024-03-18T19:48:20Z")

</div>

on a single segment i wish to threshold and mesure components. how do I manage to apply the quantification for a single level and not all levels? thank you

---

## [3D coordinate of input 3D matrix](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937)

<div class="topic-metadata">

**Author:** [@Cathy123](https://discourse.slicer.org/u/Cathy123)\
**Replies:** 5\
**Last updated:** [March 18, 2024, 7:09pm UTC](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937 "2024-03-18T19:09:09Z")

</div>

Hi, I have some problems of 3D coordinates and segmentation. what’s the coordinate relationship between 3D slicer and my volume coordinate? When I load my 3D matrix( 512512512 object) in the software, how can i set the…

---

## [Calculate Statistics with Python takes longer then with 3D Slicer GUI](https://discourse.slicer.org/t/calculate-statistics-with-python-takes-longer-then-with-3d-slicer-gui/34961)

<div class="topic-metadata">

**Author:** [@thorbenjt](https://discourse.slicer.org/u/thorbenjt)\
**Replies:** 0\
**Last updated:** [March 18, 2024, 6:23pm UTC](https://discourse.slicer.org/t/calculate-statistics-with-python-takes-longer-then-with-3d-slicer-gui/34961 "2024-03-18T18:23:30Z")

</div>

Hi there, i am currently working on a script the automates tresholding and in addition splitting the segments into islands. this works just as fine as if i would do it per hand in the 3D Slicer GUI. The critical part …

---

## [Local threshold no longer works](https://discourse.slicer.org/t/local-threshold-no-longer-works/34934)

<div class="topic-metadata">

**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 2\
**Last updated:** [March 18, 2024, 3:58pm UTC](https://discourse.slicer.org/t/local-threshold-no-longer-works/34934 "2024-03-18T15:58:33Z")

</div>

On latest Slicer preview in Linux, nothing happens in the slice views after selecting ‘Local threshold’ in the ‘Segment editor’. My oldest build is 5.7.0-2024-02-29 r32739 / c7fe865 where it does not work either. The res…

---

## [Unique color for cloned segments](https://discourse.slicer.org/t/unique-color-for-cloned-segments/34957)

<div class="topic-metadata">

**Author:** [@Yirzu](https://discourse.slicer.org/u/Yirzu)\
**Replies:** 1\
**Last updated:** [March 18, 2024, 2:53pm UTC](https://discourse.slicer.org/t/unique-color-for-cloned-segments/34957 "2024-03-18T14:53:16Z")

</div>

Hello, Color is assigned uniquely each time we add a new segment. However, this behavior does not apply when cloning segments; cloned segments appear to have the same color as the original one. How can cloned segments …

---

## [3Dslicer to three.js](https://discourse.slicer.org/t/3dslicer-to-three-js/34952)

<div class="topic-metadata">

**Author:** [@Young\_Wang](https://discourse.slicer.org/u/Young_Wang)\
**Replies:** 2\
**Last updated:** [March 18, 2024, 2:52pm UTC](https://discourse.slicer.org/t/3dslicer-to-three-js/34952 "2024-03-18T14:52:44Z")

</div>

Hi Everyone, I’ve recently started a personal project to showcase 3D volumes on the web using three.js. Currently, I’m in the process of refining my workflow, and I wanted to share my current steps with you all. I came …

---

## [Dimensions exported stl file](https://discourse.slicer.org/t/dimensions-exported-stl-file/34956)

<div class="topic-metadata">

**Author:** [@Marthe](https://discourse.slicer.org/u/Marthe)\
**Replies:** 1\
**Last updated:** [March 18, 2024, 2:09pm UTC](https://discourse.slicer.org/t/dimensions-exported-stl-file/34956 "2024-03-18T14:09:02Z")

</div>

Dear all After segmenting a body part from a CT in 3D slicer and performing a ROI cut, I exported the segmented part as an STL to make a mold in Solid Edge. However, when I open the STL file in Solid Edge, the dimension…

---

## [Problem with Segmentation UNet](https://discourse.slicer.org/t/problem-with-segmentation-unet/34923)

<div class="topic-metadata">

**Author:** [@LeidyMoraV](https://discourse.slicer.org/u/LeidyMoraV)\
**Replies:** 3\
**Last updated:** [March 18, 2024, 2:00pm UTC](https://discourse.slicer.org/t/problem-with-segmentation-unet/34923 "2024-03-18T14:00:13Z")

</div>

Hello, I’m new working with PLUS and sliceIGT and I’m trying to follow the tutorial: Tracked ultrasound AI segmentation and 3D reconstruction tutorial - YouTube But after adding the py file the ‘Ultrasound’ \> ‘Segment…

---

## [Fill between slice 3D slicer problem](https://discourse.slicer.org/t/fill-between-slice-3d-slicer-problem/34917)

<div class="topic-metadata">

**Author:** [@Simon\_Molina](https://discourse.slicer.org/u/Simon_Molina)\
**Replies:** 3\
**Last updated:** [March 18, 2024, 12:37pm UTC](https://discourse.slicer.org/t/fill-between-slice-3d-slicer-problem/34917 "2024-03-18T12:37:19Z")

</div>

Hello, I have a stent-graft geometry and I would like to fill its holes without modifying the rest of the geometry. I tried to use the fill between slice tool to do so but I can’t figure out how this works… In one of t…

[Previous page](https://discourse.slicer.org/c/support/11.md?page=105)

[Next page](https://discourse.slicer.org/c/support/11.md?page=107)