# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=216

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

**Page:** 217

---

## [Canine Liver Segmentation](https://discourse.slicer.org/t/canine-liver-segmentation/24136)

<div class="topic-metadata">

**Author:** [@sandigeeup](https://discourse.slicer.org/u/sandigeeup)\
**Replies:** 18\
**Last updated:** [July 4, 2022, 6:40pm UTC](https://discourse.slicer.org/t/canine-liver-segmentation/24136 "2022-07-04T18:40:18Z")

</div>

Hi, I am segmenting a Canine liver. Sadly, this is not as easy as segmenting a human liver as the canine liver has 4 lobes and 4 sub lobes. Also because of the way the liver is in situ, the lobes overlap and are deeply f…

---

## [Is there method segmentation using K-means and Fuzzy logic in 3D Slicer](https://discourse.slicer.org/t/is-there-method-segmentation-using-k-means-and-fuzzy-logic-in-3d-slicer/24167)

<div class="topic-metadata">

**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 1\
**Last updated:** [July 4, 2022, 12:01pm UTC](https://discourse.slicer.org/t/is-there-method-segmentation-using-k-means-and-fuzzy-logic-in-3d-slicer/24167 "2022-07-04T12:01:04Z")

</div>

Dear all, Anyone know in 3D slicer, is it have the method of fuzzy logic and K-means for tumor/lesion segmentation?

---

## [Segment Statistics Volume Calculation](https://discourse.slicer.org/t/segment-statistics-volume-calculation/3252)

<div class="topic-metadata">

**Author:** [@sboebin](https://discourse.slicer.org/u/sboebin)\
**Replies:** 8\
**Last updated:** [July 4, 2022, 7:59am UTC](https://discourse.slicer.org/t/segment-statistics-volume-calculation/3252 "2022-07-04T07:59:31Z")

</div>

Hello, I am new to Slicer and have a few questions about the Segment Statistics Module, particularly how it calculates volume. I am currently segmenting muscle groups, subcutaneous and intramuscular fat within a single s…

---

## [How to get the set data image for liver ct scan (with tumor on it)](https://discourse.slicer.org/t/how-to-get-the-set-data-image-for-liver-ct-scan-with-tumor-on-it/23995)

<div class="topic-metadata">

**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 2\
**Last updated:** [July 4, 2022, 5:06am UTC](https://discourse.slicer.org/t/how-to-get-the-set-data-image-for-liver-ct-scan-with-tumor-on-it/23995 "2022-07-04T05:06:56Z")

</div>

Dear all, Anyone know how to get the image for liver with tumor on itself. Because i want to do the liver tumor segmentation.

---

## [Over write none option gone?](https://discourse.slicer.org/t/over-write-none-option-gone/24162)

<div class="topic-metadata">

**Author:** [@sandigeeup](https://discourse.slicer.org/u/sandigeeup)\
**Replies:** 3\
**Last updated:** [July 3, 2022, 3:01pm UTC](https://discourse.slicer.org/t/over-write-none-option-gone/24162 "2022-07-03T15:01:07Z")

</div>

Hi, I am working on 4.13.0 version; Can you tell me why in threshold; the overwrite NONE option is no longer available? What do I use instead?

---

## [Possible malfunction with Slicer kernel for Jupyter notebook?](https://discourse.slicer.org/t/possible-malfunction-with-slicer-kernel-for-jupyter-notebook/24163)

<div class="topic-metadata">

**Author:** [@KateDelb](https://discourse.slicer.org/u/KateDelb)\
**Replies:** 0\
**Last updated:** [July 3, 2022, 3:00pm UTC](https://discourse.slicer.org/t/possible-malfunction-with-slicer-kernel-for-jupyter-notebook/24163 "2022-07-03T15:00:15Z")

</div>

Hi! I’m trying to import the sitkUtils package in Jupyter notebook, I’m using the 3dSlicer kernel, which has worked perfectly for me before: import sitkUtils as su In a following cell I check if su is imported, which …

---

## [Vmtk Vesselness Filtering: select seedpoint in Python](https://discourse.slicer.org/t/vmtk-vesselness-filtering-select-seedpoint-in-python/24135)

<div class="topic-metadata">

**Author:** [@KateDelb](https://discourse.slicer.org/u/KateDelb)\
**Replies:** 1\
**Last updated:** [July 3, 2022, 1:51am UTC](https://discourse.slicer.org/t/vmtk-vesselness-filtering-select-seedpoint-in-python/24135 "2022-07-03T01:51:48Z")

</div>

Hey! I’m using the VMTK VesselnessFilter to find my vessels in a T1ce image. I did this manually in 3DSlicer with no issues. However, I’m seeing that I get better results when I select a seedpoint to determine the min/…

---

## [Extraction of open-state mitral valve geometry from CT volumes --- 2018](https://discourse.slicer.org/t/extraction-of-open-state-mitral-valve-geometry-from-ct-volumes-2018/24152)

<div class="topic-metadata">

**Author:** [@whu](https://discourse.slicer.org/u/whu)\
**Replies:** 0\
**Last updated:** [July 2, 2022, 1:34am UTC](https://discourse.slicer.org/t/extraction-of-open-state-mitral-valve-geometry-from-ct-volumes-2018/24152 "2022-07-02T01:34:33Z")

</div>

As the title, that publication introduced method for segment the valve in CT volumes. But as to the US data, the steps may the same, the center of the MV, landmark for annulus, MPR, so on. Anybody can share the source …

---

## [visualization of STL surface orientation flipped between machines](https://discourse.slicer.org/t/visualization-of-stl-surface-orientation-flipped-between-machines/24148)

<div class="topic-metadata">

**Author:** [@ChantelC](https://discourse.slicer.org/u/ChantelC)\
**Replies:** 2\
**Last updated:** [July 1, 2022, 8:17pm UTC](https://discourse.slicer.org/t/visualization-of-stl-surface-orientation-flipped-between-machines/24148 "2022-07-01T20:17:35Z")

</div>

I am visualizing the output of the mri2mesh simnibs pipeline gray matter and white matter segmentation surfaces against the original mri in slicer on a mac server (mojave 10.14.6) and the .stl surfaces are flipped in ori…

---

## [No module named 'SegmentEditorMaskVolumeLib'](https://discourse.slicer.org/t/no-module-named-segmenteditormaskvolumelib/24130)

<div class="topic-metadata">

**Author:** [@jmhuie](https://discourse.slicer.org/u/jmhuie)\
**Replies:** 3\
**Last updated:** [July 1, 2022, 2:41pm UTC](https://discourse.slicer.org/t/no-module-named-segmenteditormaskvolumelib/24130 "2022-07-01T14:41:29Z")

</div>

Until recently, my extension SegmentGeometry imported the SegmentEditorMaskVolumeLib from the SegmentEditor with no problem. However, I recently updated Slicer on my computer along with the extensions and now it no longe…

---

## [An error during the extension distribution](https://discourse.slicer.org/t/an-error-during-the-extension-distribution/24027)

<div class="topic-metadata">

**Author:** [@CharlesChen](https://discourse.slicer.org/u/CharlesChen)\
**Replies:** 9\
**Last updated:** [July 1, 2022, 12:43pm UTC](https://discourse.slicer.org/t/an-error-during-the-extension-distribution/24027 "2022-07-01T12:43:08Z")

</div>

System: Win 10 Version: 5.0.2 Hello, I’m new to 3DSlicer, I developed a python scripted extension, which is for computing the percentage of colocalization(Spatial overlap between different channels) of Z-stack TIFF im…

---

## [Rotation matrix from the Transform Module](https://discourse.slicer.org/t/rotation-matrix-from-the-transform-module/7103)

<div class="topic-metadata">

**Author:** [@Mary7291](https://discourse.slicer.org/u/Mary7291)\
**Replies:** 16\
**Last updated:** [July 1, 2022, 9:06am UTC](https://discourse.slicer.org/t/rotation-matrix-from-the-transform-module/7103 "2022-07-01T09:06:32Z")

</div>

Operating system: windows 7 Slicer version: 4.8.1 Expected behavior: Actual behavior: Hello, I create a needle model to insert it to a specific region in my 3D model in slicer. This way, the position of the needle t…

---

## [How to change render window plane programmingly?](https://discourse.slicer.org/t/how-to-change-render-window-plane-programmingly/24111)

<div class="topic-metadata">

**Author:** [@user4](https://discourse.slicer.org/u/user4)\
**Replies:** 4\
**Last updated:** [July 1, 2022, 7:06am UTC](https://discourse.slicer.org/t/how-to-change-render-window-plane-programmingly/24111 "2022-07-01T07:06:02Z")

</div>

Hi,all. I want to change the view plane in render window using python,as marked in red box here. That is to say,If I click the P-A orientation,I can get a Coronal plane of the image, I want to use few lines of code t…

---

## [Model maker input volume problem](https://discourse.slicer.org/t/model-maker-input-volume-problem/24126)

<div class="topic-metadata">

**Author:** [@canseda](https://discourse.slicer.org/u/canseda)\
**Replies:** 2\
**Last updated:** [June 30, 2022, 11:55pm UTC](https://discourse.slicer.org/t/model-maker-input-volume-problem/24126 "2022-06-30T23:55:26Z")

</div>

Problem report for Slicer 5.0.2 macosx-amd64: Hi, I’ve started use Slicer. Unfortunately, whenever I try to perform ‘model maker’ stage, after segmentation, the system gives error ‘cannot open input volume file…’. I watc…

---

## [Is it possible to place markup points and pass them to a slicer executable module I have created?](https://discourse.slicer.org/t/is-it-possible-to-place-markup-points-and-pass-them-to-a-slicer-executable-module-i-have-created/24108)

<div class="topic-metadata">

**Author:** [@Kevin.Kn](https://discourse.slicer.org/u/Kevin.Kn)\
**Replies:** 5\
**Last updated:** [June 30, 2022, 8:53pm UTC](https://discourse.slicer.org/t/is-it-possible-to-place-markup-points-and-pass-them-to-a-slicer-executable-module-i-have-created/24108 "2022-06-30T20:53:25Z")

</div>

I currently have been using ITK to generate automated segmentations using command line inputs that include seed point regions of interest, to create a more efficient version of outdated matlab code that my lab is using. …

---

## [Tractography issue](https://discourse.slicer.org/t/tractography-issue/24093)

<div class="topic-metadata">

**Author:** [@massimo](https://discourse.slicer.org/u/massimo)\
**Replies:** 4\
**Last updated:** [June 30, 2022, 6:21pm UTC](https://discourse.slicer.org/t/tractography-issue/24093 "2022-06-30T18:21:55Z")

</div>

Operating system: Mac OSX Monterey Slicer version:5.0.2 Expected behavior: Tractography visualization Actual behavior: Errors in data import Dear Community, I’m trying to create a 3d model of a tractography to view …

---

## [Fixes label for dicom image](https://discourse.slicer.org/t/fixes-label-for-dicom-image/24116)

<div class="topic-metadata">

**Author:** [@Van\_Tran\_Sang\_Huynh](https://discourse.slicer.org/u/Van_Tran_Sang_Huynh)\
**Replies:** 0\
**Last updated:** [June 30, 2022, 12:09pm UTC](https://discourse.slicer.org/t/fixes-label-for-dicom-image/24116 "2022-06-30T12:09:18Z")

</div>

I use dicom dataset for feature extraction. But I got an error about ‘label’. Hoping for help from future import print\_function import six import os # needed navigate the system to get the input data import matplotl…

---

## [Adjusting the contrast](https://discourse.slicer.org/t/adjusting-the-contrast/24113)

<div class="topic-metadata">

**Author:** [@sandigeeup](https://discourse.slicer.org/u/sandigeeup)\
**Replies:** 2\
**Last updated:** [June 30, 2022, 10:13am UTC](https://discourse.slicer.org/t/adjusting-the-contrast/24113 "2022-06-30T10:13:41Z")

</div>

For some reason I can’t adjust the contrast in my Dicom images since I upgraded to the latest slicer, is this an issue for anyone else?

---

## [how to rotate camer on a reslice image and change the image display?](https://discourse.slicer.org/t/how-to-rotate-camer-on-a-reslice-image-and-change-the-image-display/8611)

<div class="topic-metadata">

**Author:** [@pingdan](https://discourse.slicer.org/u/pingdan)\
**Replies:** 3\
**Last updated:** [June 30, 2022, 7:41am UTC](https://discourse.slicer.org/t/how-to-rotate-camer-on-a-reslice-image-and-change-the-image-display/8611 "2022-06-30T07:41:14Z")

</div>

I display a image in renderer, and rotate some degree of camera, but the image of displaying don’t have difference. after rotation, I got the parameter of image, it has changed. vtkSmartPointer reader = vtkSmartPointer:…

---

## [Is there a automatic heart segmentation tool that can be used, similar to the ribcage](https://discourse.slicer.org/t/is-there-a-automatic-heart-segmentation-tool-that-can-be-used-similar-to-the-ribcage/24066)

<div class="topic-metadata">

**Author:** [@Monkeyking123](https://discourse.slicer.org/u/Monkeyking123)\
**Replies:** 3\
**Last updated:** [June 30, 2022, 1:37am UTC](https://discourse.slicer.org/t/is-there-a-automatic-heart-segmentation-tool-that-can-be-used-similar-to-the-ribcage/24066 "2022-06-30T01:37:41Z")

</div>

As in the aforementioned title, \*\*Is there an automatic heart segmentation tool for segmenting the important heart structures: Left/Right (Ventricle/Atrium) , Superior/inferior vena cava/pulmonary artery etc Since som…

---

## [Can't find module after installing extension](https://discourse.slicer.org/t/cant-find-module-after-installing-extension/24018)

<div class="topic-metadata">

**Author:** [@vyvyvyvy](https://discourse.slicer.org/u/vyvyvyvy)\
**Replies:** 6\
**Last updated:** [June 29, 2022, 3:41pm UTC](https://discourse.slicer.org/t/cant-find-module-after-installing-extension/24018 "2022-06-29T15:41:43Z")

</div>

I installed the SlicerVMTK extension (manual installation) and the relevant modules were not found in the dropdown list. How can I resolve this issue? I currently have the latest version (5.0.2) installed.

---

## [Fast marching problem ver 5.0.2](https://discourse.slicer.org/t/fast-marching-problem-ver-5-0-2/24078)

<div class="topic-metadata">

**Author:** [@Nguyen\_Hieu](https://discourse.slicer.org/u/Nguyen_Hieu)\
**Replies:** 1\
**Last updated:** [June 28, 2022, 4:26pm UTC](https://discourse.slicer.org/t/fast-marching-problem-ver-5-0-2/24078 "2022-06-28T16:26:53Z")

</div>

Operating system: Windows 10 Slicer version: 5.0.2 I use this version and install Fast Marching but this extension is not appeared in “Segment Editor”, its interface is quite different from this video Fast marching seg…

---

## [LungCTAnalyzer error: Input lung CT is invalid](https://discourse.slicer.org/t/lungctanalyzer-error-input-lung-ct-is-invalid/23935)

<div class="topic-metadata">

**Author:** [@ashipde](https://discourse.slicer.org/u/ashipde)\
**Replies:** 26\
**Last updated:** [June 29, 2022, 6:33am UTC](https://discourse.slicer.org/t/lungctanalyzer-error-input-lung-ct-is-invalid/23935 "2022-06-29T06:33:41Z")

</div>

Hello, I am a novice user of 3D Slicer and trying to use version 5.0.2 of the software in macOS 10.12. For a CT that I am looking at, I could get segmentation done, but at the next step, Analyzer shows error message: Fa…

---

## [How to convert a segmentation back into a stack of images ](https://discourse.slicer.org/t/how-to-convert-a-segmentation-back-into-a-stack-of-images/24085)

<div class="topic-metadata">

**Author:** [@sam.seq](https://discourse.slicer.org/u/sam.seq)\
**Replies:** 5\
**Last updated:** [June 29, 2022, 4:46am UTC](https://discourse.slicer.org/t/how-to-convert-a-segmentation-back-into-a-stack-of-images/24085 "2022-06-29T04:46:34Z")

</div>

How do you convert a segmentation that has been edited back into a stack of images?

---

## [LungCTAnalyzer in macOS: missing os.startfile](https://discourse.slicer.org/t/lungctanalyzer-in-macos-missing-os-startfile/24058)

<div class="topic-metadata">

**Author:** [@ashipde](https://discourse.slicer.org/u/ashipde)\
**Replies:** 7\
**Last updated:** [June 29, 2022, 1:19am UTC](https://discourse.slicer.org/t/lungctanalyzer-in-macos-missing-os-startfile/24058 "2022-06-29T01:19:52Z")

</div>

@rbumm In LungCTAnalyzer 2.49 in Slicer 5.0.2 in macOS 12.4 with Python 3.9.10, when generating PDF report: report is generated in LungCTAnalyzerReports but Python Interactor shows modules/LungCTAnalyzer.py", line 843,…

---

## [How to Show a particular segment in the image highlighted](https://discourse.slicer.org/t/how-to-show-a-particular-segment-in-the-image-highlighted/18705)

<div class="topic-metadata">

**Author:** [@tpvagenas](https://discourse.slicer.org/u/tpvagenas)\
**Replies:** 8\
**Last updated:** [June 28, 2022, 4:13pm UTC](https://discourse.slicer.org/t/how-to-show-a-particular-segment-in-the-image-highlighted/18705 "2022-06-28T16:13:09Z")

</div>

Hello, I need to correct some manual segmentations I had received for the project I am working on as part of my PhD thesis. The problem is that I have a volume file and a segmentation file and the segmentation file has 2…

---

## [Segmentation of thin vessels](https://discourse.slicer.org/t/segmentation-of-thin-vessels/24082)

<div class="topic-metadata">

**Author:** [@sannpeterson](https://discourse.slicer.org/u/sannpeterson)\
**Replies:** 1\
**Last updated:** [June 27, 2022, 7:16pm UTC](https://discourse.slicer.org/t/segmentation-of-thin-vessels/24082 "2022-06-27T19:16:10Z")

</div>

Thank you for the suggestion. Can you give me tips for smaller vessels? Some arteries are very thin and hypoplastic. More automated methods tend to miss these types of vessels.

---

## [SlicerDensityLungSegmentation – using GMM model generated with older scikit-learn](https://discourse.slicer.org/t/slicerdensitylungsegmentation-using-gmm-model-generated-with-older-scikit-learn/24071)

<div class="topic-metadata">

**Author:** [@ashipde](https://discourse.slicer.org/u/ashipde)\
**Replies:** 1\
**Last updated:** [June 28, 2022, 7:30am UTC](https://discourse.slicer.org/t/slicerdensitylungsegmentation-using-gmm-model-generated-with-older-scikit-learn/24071 "2022-06-28T07:30:49Z")

</div>

I am testing the DensityLungSegmentation extension, as available in Extension Manager in Slicer 5.0.2 in Python 3.9.10/macOS 12.4 setting. It seems the precomputed GMM model that the extension uses was generated with som…

---

## [Slicer Jupyter docker with CUDA](https://discourse.slicer.org/t/slicer-jupyter-docker-with-cuda/23519)

<div class="topic-metadata">

**Author:** [@Jakub\_Mitura](https://discourse.slicer.org/u/Jakub_Mitura)\
**Replies:** 6\
**Last updated:** [June 28, 2022, 6:22am UTC](https://discourse.slicer.org/t/slicer-jupyter-docker-with-cuda/23519 "2022-06-28T06:22:50Z")

</div>

Hello I try to customize official slicer docker for jupyter, and integrate it with vs code development in a container. I managed already to Install and test CUDA - which seem to works ok (pytorch detects it) Now I have…

---

## [Qt creator can't see execution files after building from source](https://discourse.slicer.org/t/qt-creator-cant-see-execution-files-after-building-from-source/14688)

<div class="topic-metadata">

**Author:** [@keri](https://discourse.slicer.org/u/keri)\
**Replies:** 8\
**Last updated:** [June 28, 2022, 6:15am UTC](https://discourse.slicer.org/t/qt-creator-cant-see-execution-files-after-building-from-source/14688 "2022-06-28T06:15:41Z")

</div>

Hi, I built Slicer from source in debug mode. Now I’m trying to work with Slicer as with usual project but Qt creator can’t see any execution file and moreover header files are inactive like in the picture below: I …

[Previous page](https://discourse.slicer.org/c/support/11.md?page=215)

[Next page](https://discourse.slicer.org/c/support/11.md?page=217)