# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=334

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

**Page:** 335

---

## [How to automatically segment multiple lumbar vertebrae thorugh the Python Interactor?](https://discourse.slicer.org/t/how-to-automatically-segment-multiple-lumbar-vertebrae-thorugh-the-python-interactor/12198)

<div class="topic-metadata">

**Author:** [@vertebra](https://discourse.slicer.org/u/vertebra)\
**Replies:** 3\
**Last updated:** [June 26, 2020, 2:04am UTC](https://discourse.slicer.org/t/how-to-automatically-segment-multiple-lumbar-vertebrae-thorugh-the-python-interactor/12198 "2020-06-26T02:04:59Z")

</div>

We have been researching and able to finally segment all the lumbar vertebrae manually(but we used scissors and erase, something Python cannot do on a case by case basis). We seek assistance in now automating that proces…

---

## [Model To Label Map in 4.11 vs 4.10](https://discourse.slicer.org/t/model-to-label-map-in-4-11-vs-4-10/12222)

<div class="topic-metadata">

**Author:** [@siaeleni](https://discourse.slicer.org/u/siaeleni)\
**Replies:** 2\
**Last updated:** [June 25, 2020, 11:22pm UTC](https://discourse.slicer.org/t/model-to-label-map-in-4-11-vs-4-10/12222 "2020-06-25T23:22:04Z")

</div>

Hi all, I am using “Model To Label Map” built-in module in 4.11 and 4.10 and get different results. First of all, my Model is saved as “vtk output SPACE=LPS” and at 4.11 I force it to open as LPS, but I realize that wh…

---

## [How to get segmentations as numpy arrays with same dimensions?](https://discourse.slicer.org/t/how-to-get-segmentations-as-numpy-arrays-with-same-dimensions/12202)

<div class="topic-metadata">

**Author:** [@SummerZ2020](https://discourse.slicer.org/u/SummerZ2020)\
**Replies:** 7\
**Last updated:** [June 25, 2020, 2:57pm UTC](https://discourse.slicer.org/t/how-to-get-segmentations-as-numpy-arrays-with-same-dimensions/12202 "2020-06-25T14:57:14Z")

</div>

hello, lassoan. I encountered the same problem when save the segmentation result to file. I right clicked the segmentation in the “Subject hierarchy”, and then choose “export visible segments to binary labelmap”, and got…

---

## [Image is not aligned with segmentation](https://discourse.slicer.org/t/image-is-not-aligned-with-segmentation/12190)

<div class="topic-metadata">

**Author:** [@Gourav\_Modanwal](https://discourse.slicer.org/u/Gourav_Modanwal)\
**Replies:** 2\
**Last updated:** [June 25, 2020, 5:58am UTC](https://discourse.slicer.org/t/image-is-not-aligned-with-segmentation/12190 "2020-06-25T05:58:42Z")

</div>

---

## [How do we extract the features for each independent object in an image?](https://discourse.slicer.org/t/how-do-we-extract-the-features-for-each-independent-object-in-an-image/12120)

<div class="topic-metadata">

**Author:** [@mozdag](https://discourse.slicer.org/u/mozdag)\
**Replies:** 5\
**Last updated:** [June 25, 2020, 5:45am UTC](https://discourse.slicer.org/t/how-do-we-extract-the-features-for-each-independent-object-in-an-image/12120 "2020-06-25T05:45:38Z")

</div>

I have a tissue image and there are around 100 cells in it. I also have the corresponding mask image which includes those 100 cells. How do I calculate the radiomics features for each cell?

---

## [List of removed extensions now available](https://discourse.slicer.org/t/list-of-removed-extensions-now-available/12210)

<div class="topic-metadata">

**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 0\
**Last updated:** [June 25, 2020, 12:19am UTC](https://discourse.slicer.org/t/list-of-removed-extensions-now-available/12210 "2020-06-25T00:19:19Z")

</div>

Building on the prior work done by @hjmjohnson, we now have a complete list of extensions that have been removed from the extensions manager. The list also includes Date and Commit associated with the removal. See Exte…

---

## [Bad allocation exception](https://discourse.slicer.org/t/bad-allocation-exception/12172)

<div class="topic-metadata">

**Author:** [@SummerZ2020](https://discourse.slicer.org/u/SummerZ2020)\
**Replies:** 5\
**Last updated:** [June 24, 2020, 4:33pm UTC](https://discourse.slicer.org/t/bad-allocation-exception/12172 "2020-06-24T16:33:33Z")

</div>

Operating system:windows Slicer version:4.11 2020-6-15 Expected behavior:The segment operation can be done successfully. Actual behavior: bad allocation exception popped up. I add a CT image volume which contains 274…

---

## [How to change what images appear in input field of modules](https://discourse.slicer.org/t/how-to-change-what-images-appear-in-input-field-of-modules/12197)

<div class="topic-metadata">

**Author:** [@Tami](https://discourse.slicer.org/u/Tami)\
**Replies:** 3\
**Last updated:** [June 24, 2020, 3:22pm UTC](https://discourse.slicer.org/t/how-to-change-what-images-appear-in-input-field-of-modules/12197 "2020-06-24T15:22:59Z")

</div>

Operating system: Windows 10 Slicer version: 4.10.2 Expected behavior: I need to erase all my previously-loaded DICOM files from wherever they are saved, so that I will not see them under the “Input Image (or Volume)”…

---

## [Why are my segmentations being saved as only the bounding box size rather than the size of the original image?](https://discourse.slicer.org/t/why-are-my-segmentations-being-saved-as-only-the-bounding-box-size-rather-than-the-size-of-the-original-image/9909)

<div class="topic-metadata">

**Author:** [@LisaDuff](https://discourse.slicer.org/u/LisaDuff)\
**Replies:** 4\
**Last updated:** [February 11, 2020, 2:46pm UTC](https://discourse.slicer.org/t/why-are-my-segmentations-being-saved-as-only-the-bounding-box-size-rather-than-the-size-of-the-original-image/9909 "2020-02-11T14:46:14Z")

</div>

hi I have made a large amount of segmentations on 3D slicer but when I try to save them they are only the size of the area covered by the segmentation. For example if the segmentation covers 100x40x40 slices it only sav…

---

## [Vertebra Segmentation](https://discourse.slicer.org/t/vertebra-segmentation/12183)

<div class="topic-metadata">

**Author:** [@vertebra](https://discourse.slicer.org/u/vertebra)\
**Replies:** 2\
**Last updated:** [June 23, 2020, 11:29pm UTC](https://discourse.slicer.org/t/vertebra-segmentation/12183 "2020-06-23T23:29:08Z")

</div>

Operating system: Mac Slicer version: 4.10.2 Expected behavior: I am trying to segment the vertebra into individual vertebrae. The 3D slicer allows me to threshold relatively easily and isolate the backbone. However, t…

---

## ["Unable to open OpenCV video device" error when streaming an URL using PLUS Toolkit](https://discourse.slicer.org/t/unable-to-open-opencv-video-device-error-when-streaming-an-url-using-plus-toolkit/12188)

<div class="topic-metadata">

**Author:** [@xlucia](https://discourse.slicer.org/u/xlucia)\
**Replies:** 0\
**Last updated:** [June 23, 2020, 9:59pm UTC](https://discourse.slicer.org/t/unable-to-open-opencv-video-device-error-when-streaming-an-url-using-plus-toolkit/12188 "2020-06-23T21:59:14Z")

</div>

Hello! I am trying to stream an URL using the following PLUS config file (I want to send the video from the streaming to SlicerIGT): …

---

## [Problems applying texture to model in 4.11 version](https://discourse.slicer.org/t/problems-applying-texture-to-model-in-4-11-version/12180)

<div class="topic-metadata">

**Author:** [@lauraflores98](https://discourse.slicer.org/u/lauraflores98)\
**Replies:** 2\
**Last updated:** [June 23, 2020, 6:55pm UTC](https://discourse.slicer.org/t/problems-applying-texture-to-model-in-4-11-version/12180 "2020-06-23T18:55:26Z")

</div>

Operating system: macOS catalina 10.15.3 Slicer version: 4.11.0 Expected behavior: I’m programming an extension. On it, I load a back scan (both the volume as a .obj and the texture as .jpg) and later on apply the t…

---

## [Curve visible in 2D views?](https://discourse.slicer.org/t/curve-visible-in-2d-views/12020)

<div class="topic-metadata">

**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 6\
**Last updated:** [June 23, 2020, 4:59pm UTC](https://discourse.slicer.org/t/curve-visible-in-2d-views/12020 "2020-06-23T16:59:23Z")

</div>

This is probably for Andras (@lassoan). When I make an open curve by placing points, I generally do it using a custom layout of stacked 3D views with various layers visible. I noticed this morning when I switched to 4-up…

---

## [How to create a Collapsible button in a python 3.7 GUI](https://discourse.slicer.org/t/how-to-create-a-collapsible-button-in-a-python-3-7-gui/12177)

<div class="topic-metadata">

**Author:** [@xlucox](https://discourse.slicer.org/u/xlucox)\
**Replies:** 1\
**Last updated:** [June 23, 2020, 3:25pm UTC](https://discourse.slicer.org/t/how-to-create-a-collapsible-button-in-a-python-3-7-gui/12177 "2020-06-23T15:25:08Z")

</div>

Hi !!! I’m developing an application in python 3.7 using qt and I would like to create a collapsible button as the used in 3D slicer (ctk.ctkCollapsibleButton()). I tried to download ctk but it seems to don’t have this …

---

## [DICOM segmentation import problem on Windows](https://discourse.slicer.org/t/dicom-segmentation-import-problem-on-windows/12084)

<div class="topic-metadata">

**Author:** [@laurenz](https://discourse.slicer.org/u/laurenz)\
**Replies:** 8\
**Last updated:** [June 23, 2020, 2:12am UTC](https://discourse.slicer.org/t/dicom-segmentation-import-problem-on-windows/12084 "2020-06-23T02:12:49Z")

</div>

I am trying to view DICOM segmentations on slicer as an overlay on PET and CT images. The DICOM segmentations won’t load. I have tried uninstalling and reinstalling the extensions one by one as well as all at once. The P…

---

## [SlicerRT DICOM RT import issue](https://discourse.slicer.org/t/slicerrt-dicom-rt-import-issue/11881)

<div class="topic-metadata">

**Author:** [@martin](https://discourse.slicer.org/u/martin)\
**Replies:** 4\
**Last updated:** [June 23, 2020, 2:11am UTC](https://discourse.slicer.org/t/slicerrt-dicom-rt-import-issue/11881 "2020-06-23T02:11:30Z")

</div>

Hello All, I tried to import the DICOM RT in 3Dslicer with SlicerRT module, however the log shows the module seems have some issues. I have tried to reinstall the 3dSlicer and the SlicerRT module, but the error still ap…

---

## [NvidiaAIAssistedAnnotation extension for macOS](https://discourse.slicer.org/t/nvidiaaiassistedannotation-extension-for-macos/12158)

<div class="topic-metadata">

**Author:** [@Lorena](https://discourse.slicer.org/u/Lorena)\
**Replies:** 1\
**Last updated:** [June 22, 2020, 5:16pm UTC](https://discourse.slicer.org/t/nvidiaaiassistedannotation-extension-for-macos/12158 "2020-06-22T17:16:34Z")

</div>

Operating system: macOS Catalina version 10.15.5 Slicer version: 4.11.0, revision 29163, built 2020-6-22 (as of https://download.slicer.org) Expected behavior: open Extensions Manager and install NvidiaAIAssistedAnnota…

---

## [Virtual Fracture Reconstruction Extension](https://discourse.slicer.org/t/virtual-fracture-reconstruction-extension/10587)

<div class="topic-metadata">

**Author:** [@kt297](https://discourse.slicer.org/u/kt297)\
**Replies:** 5\
**Last updated:** [June 21, 2020, 3:23pm UTC](https://discourse.slicer.org/t/virtual-fracture-reconstruction-extension/10587 "2020-06-21T15:23:58Z")

</div>

How do I install this Virtual Fracture reconstruction module into 3d Slicer? There doesn’t seem to be an extension for it within 3D slicer? Here is the link: https://www.slicer.org/wiki/Documentation/Nightly/Extensions/…

---

## [Using crop volume module to extract subvolume from a 3D volume](https://discourse.slicer.org/t/using-crop-volume-module-to-extract-subvolume-from-a-3d-volume/11926)

<div class="topic-metadata">

**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 5\
**Last updated:** [June 20, 2020, 9:52pm UTC](https://discourse.slicer.org/t/using-crop-volume-module-to-extract-subvolume-from-a-3d-volume/11926 "2020-06-20T21:52:39Z")

</div>

Hello Everyone, I have a 3D volume like the following that has been reconstructed from 2D images. I’d like to know if there is a way to remove the terminal branches from this volume . By terminal branches, I mean the…

---

## [Centerline computation failed](https://discourse.slicer.org/t/centerline-computation-failed/11981)

<div class="topic-metadata">

**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 10\
**Last updated:** [June 20, 2020, 9:51pm UTC](https://discourse.slicer.org/t/centerline-computation-failed/11981 "2020-06-20T21:51:57Z")

</div>

Hello Everyone, I’ve been trying to compute centerlines for this geometry using VMTK extension. However, I couldn’t successfully obtain centerlines. Even the networkExtraction failed when I tried to use the stl file o…

---

## [Computational Centerline Error](https://discourse.slicer.org/t/computational-centerline-error/12039)

<div class="topic-metadata">

**Author:** [@Madelene\_Habib](https://discourse.slicer.org/u/Madelene_Habib)\
**Replies:** 6\
**Last updated:** [June 20, 2020, 9:39pm UTC](https://discourse.slicer.org/t/computational-centerline-error/12039 "2020-06-20T21:39:11Z")

</div>

Hello, I’m running into this issue when I press “preview” in the SlicerVMTK Centerline Computation module.

---

## [Build Issue with Slicer-4.10.2 on centOS8](https://discourse.slicer.org/t/build-issue-with-slicer-4-10-2-on-centos8/12101)

<div class="topic-metadata">

**Author:** [@DavidCai1246](https://discourse.slicer.org/u/DavidCai1246)\
**Replies:** 5\
**Last updated:** [June 20, 2020, 3:47am UTC](https://discourse.slicer.org/t/build-issue-with-slicer-4-10-2-on-centos8/12101 "2020-06-20T03:47:53Z")

</div>

Operating system: centOS8 Slicer version: 4.10.2 I’m following the instructions on nightly build. However when I start building the slicer, I get the following error: \[ 10%\] No install step for ‘DCMTK’ \[ 10%\] Comple…

---

## [Uploading Dicoms](https://discourse.slicer.org/t/uploading-dicoms/12124)

<div class="topic-metadata">

**Author:** [@wrightt](https://discourse.slicer.org/u/wrightt)\
**Replies:** 1\
**Last updated:** [June 19, 2020, 8:31pm UTC](https://discourse.slicer.org/t/uploading-dicoms/12124 "2020-06-19T20:31:44Z")

</div>

Operating system: Windows 10 Slicer version: 4.10.2 Expected behavior: Uploaded DICOM Files Actual behavior: No DICOM datasets load to the program I am having trouble uploading my DICOM files (RA64) to the 3D Slicer …

---

## [Load curvenodes from stl/vtk file](https://discourse.slicer.org/t/load-curvenodes-from-stl-vtk-file/12091)

<div class="topic-metadata">

**Author:** [@Neda](https://discourse.slicer.org/u/Neda)\
**Replies:** 2\
**Last updated:** [June 19, 2020, 4:46pm UTC](https://discourse.slicer.org/t/load-curvenodes-from-stl-vtk-file/12091 "2020-06-19T16:46:42Z")

</div>

Hi, I am using 3D slicer 4.11.0 for analyzing dental CT. I need a bunch of points around mandible curve to compute a panoramic X-ray from a cone-beam dental CT (https://gist.github.com/lassoan/b445c734f118a5fb7643f3fb05…

---

## [Volume Information for Proper Ruler Calibration](https://discourse.slicer.org/t/volume-information-for-proper-ruler-calibration/12109)

<div class="topic-metadata">

**Author:** [@Angel](https://discourse.slicer.org/u/Angel)\
**Replies:** 2\
**Last updated:** [June 19, 2020, 4:21pm UTC](https://discourse.slicer.org/t/volume-information-for-proper-ruler-calibration/12109 "2020-06-19T16:21:27Z")

</div>

Hello, I have been trying to use Slicer to take measurements using the ruler tool on JPEG images of a chicken embryo heart. The heart is only about 5 mm across and I have been getting measurements around 300 mm across t…

---

## [Slicer cache settings](https://discourse.slicer.org/t/slicer-cache-settings/12112)

<div class="topic-metadata">

**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 1\
**Last updated:** [June 19, 2020, 1:42pm UTC](https://discourse.slicer.org/t/slicer-cache-settings/12112 "2020-06-19T13:42:08Z")

</div>

Hi All, Would it help if the default cache size is changed while facing memory issues

---

## [Segmented using deep learning](https://discourse.slicer.org/t/segmented-using-deep-learning/12086)

<div class="topic-metadata">

**Author:** [@khikho](https://discourse.slicer.org/u/khikho)\
**Replies:** 1\
**Last updated:** [June 18, 2020, 9:36pm UTC](https://discourse.slicer.org/t/segmented-using-deep-learning/12086 "2020-06-18T21:36:04Z")

</div>

HI • I have a problem when running TOMAAT not running and exiting ? • I installed DeepInfer and that’s next steps ((extensions manager + install + restart)) But when I go to the front slicer 3d, I can’t find it ? •…

---

## [vtkDebug Leaks caused by storage node](https://discourse.slicer.org/t/vtkdebug-leaks-caused-by-storage-node/12094)

<div class="topic-metadata">

**Author:** [@Queen\_Rei](https://discourse.slicer.org/u/Queen_Rei)\
**Replies:** 6\
**Last updated:** [June 18, 2020, 8:08pm UTC](https://discourse.slicer.org/t/vtkdebug-leaks-caused-by-storage-node/12094 "2020-06-18T20:08:22Z")

</div>

Hello! I am trying to resolve some leaks that are related to the following lines. This script is meant to run the module 100 ms after start-up and when I remove this snippet the errors go away. Is there a flaw in the wa…

---

## [import slicer in a local python/virtualenv and load correctly image orientation](https://discourse.slicer.org/t/import-slicer-in-a-local-python-virtualenv-and-load-correctly-image-orientation/12092)

<div class="topic-metadata">

**Author:** [@emiltoft](https://discourse.slicer.org/u/emiltoft)\
**Replies:** 1\
**Last updated:** [June 18, 2020, 5:39pm UTC](https://discourse.slicer.org/t/import-slicer-in-a-local-python-virtualenv-and-load-correctly-image-orientation/12092 "2020-06-18T17:39:51Z")

</div>

Is it possible to use slicer’s python api in a custom made program? Specifically, am I interested in the dicom-image loading due to the correctly dicom volume-image orientation. I have can see in previous posts that it’…

---

## [How, via python scripts, to hide the image name?](https://discourse.slicer.org/t/how-via-python-scripts-to-hide-the-image-name/12085)

<div class="topic-metadata">

**Author:** [@aiden.zhu](https://discourse.slicer.org/u/aiden.zhu)\
**Replies:** 2\
**Last updated:** [June 18, 2020, 1:24pm UTC](https://discourse.slicer.org/t/how-via-python-scripts-to-hide-the-image-name/12085 "2020-06-18T13:24:37Z")

</div>

Operating system: windows Slicer version: 4.11.0 Expected behavior: hide image name Actual behavior: Sometimes I would like to have an automatic screen shot of view without any image names. How to do it via python? T…

[Previous page](https://discourse.slicer.org/c/support/11.md?page=333)

[Next page](https://discourse.slicer.org/c/support/11.md?page=335)