# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=324

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

**Page:** 325

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## [Elastix 2d/3d Registration Incorrect Ray Cast](https://discourse.slicer.org/t/elastix-2d-3d-registration-incorrect-ray-cast/13243)

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**Author:** [@Henry\_Cope](https://discourse.slicer.org/u/Henry_Cope)\
**Replies:** 3\
**Last updated:** [August 31, 2020, 8:54pm UTC](https://discourse.slicer.org/t/elastix-2d-3d-registration-incorrect-ray-cast/13243 "2020-08-31T20:54:55Z")

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Good Evening, I’m trying to use the general registration elastix module to register a 3d CT volume I have to an Xray. Before trying my data, I used the 2d/3d test data that comes with Elastix. I tried to register a volu…

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## [trouble viewing my files](https://discourse.slicer.org/t/trouble-viewing-my-files/13253)

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**Author:** [@bob](https://discourse.slicer.org/u/bob)\
**Replies:** 4\
**Last updated:** [August 31, 2020, 5:54pm UTC](https://discourse.slicer.org/t/trouble-viewing-my-files/13253 "2020-08-31T17:54:39Z")

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I have watched a couple of youtube introductions to 3D Slicer, but am having challenges to get my .DCM files to display properly. Either no image appears or I see collapsed views. Any suggestions how to work past this? …

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## [How to include qwidgets in slicer qml layout](https://discourse.slicer.org/t/how-to-include-qwidgets-in-slicer-qml-layout/13259)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 1\
**Last updated:** [August 31, 2020, 5:52pm UTC](https://discourse.slicer.org/t/how-to-include-qwidgets-in-slicer-qml-layout/13259 "2020-08-31T17:52:28Z")

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I am using this layout. I want to insert a toolbar on top of first viewNode only. That means at grid(0,0) position I want a layout which contains both toolbar and viewNode1. How can I do this?

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## [How to hold the imageWidget display](https://discourse.slicer.org/t/how-to-hold-the-imagewidget-display/13246)

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**Author:** [@aiden.zhu](https://discourse.slicer.org/u/aiden.zhu)\
**Replies:** 2\
**Last updated:** [August 31, 2020, 2:10pm UTC](https://discourse.slicer.org/t/how-to-hold-the-imagewidget-display/13246 "2020-08-31T14:10:34Z")

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Operating system: windows Slicer version: 4.11.0 Expected behavior: show() to have the image shown Actual behavior: the image flashed and disappear Hi all, I tried the following scripts, https://www.slicer.org/wiki…

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## [Get labelmap from each segment separately?](https://discourse.slicer.org/t/get-labelmap-from-each-segment-separately/13231)

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**Author:** [@44REAM](https://discourse.slicer.org/u/44REAM)\
**Replies:** 2\
**Last updated:** [August 31, 2020, 10:49am UTC](https://discourse.slicer.org/t/get-labelmap-from-each-segment-separately/13231 "2020-08-31T10:49:35Z")

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I try to convert segmentation to labelmap separately from cli (eg labelmap of body, lung\_L and lung\_R separately). I found that this code below can export visable segment to labelmap. seg = getNode(‘Segmentation’) re…

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## [Recent improvements in window/level management](https://discourse.slicer.org/t/recent-improvements-in-window-level-management/7284)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 9\
**Last updated:** [August 31, 2020, 5:19am UTC](https://discourse.slicer.org/t/recent-improvements-in-window-level-management/7284 "2020-08-31T05:19:26Z")

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This is a quick summary of image window/level (brightness/contrast) adjustment changes introduced in recent Slicer Preview (formerly known as “Nightly”) releases. Improved automatic window/level algorithm Images that …

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## [fusion of different sequencies and segmentation mask after editing in one study dicom extension](https://discourse.slicer.org/t/fusion-of-different-sequencies-and-segmentation-mask-after-editing-in-one-study-dicom-extension/13242)

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**Author:** [@haytham\_Nasser](https://discourse.slicer.org/u/haytham_Nasser)\
**Replies:** 1\
**Last updated:** [August 31, 2020, 1:24am UTC](https://discourse.slicer.org/t/fusion-of-different-sequencies-and-segmentation-mask-after-editing-in-one-study-dicom-extension/13242 "2020-08-31T01:24:52Z")

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Operating system: windows Slicer version: Expected behavior: Actual behavior:

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## [Created an STL file from numpy array but unable to get this aligned with dicom volume after loading](https://discourse.slicer.org/t/created-an-stl-file-from-numpy-array-but-unable-to-get-this-aligned-with-dicom-volume-after-loading/13174)

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**Author:** [@Gabriel\_T](https://discourse.slicer.org/u/Gabriel_T)\
**Replies:** 3\
**Last updated:** [August 31, 2020, 1:22am UTC](https://discourse.slicer.org/t/created-an-stl-file-from-numpy-array-but-unable-to-get-this-aligned-with-dicom-volume-after-loading/13174 "2020-08-31T01:22:29Z")

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I have a binary segmentation mask, I converted this to an STL file. I converted to mm space from pixel coordinate space by Finding the coordinates of the vertices using marching cubes lewinn algorithm from skimage mult…

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## [Segment editor / Split volume : Fill value is ignored](https://discourse.slicer.org/t/segment-editor-split-volume-fill-value-is-ignored/13237)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 1\
**Last updated:** [August 30, 2020, 4:22pm UTC](https://discourse.slicer.org/t/segment-editor-split-volume-fill-value-is-ignored/13237 "2020-08-30T16:22:00Z")

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In Segment editor / Split volume module, the specified Fill Value is ignored and is always set to 0 in the output volume. That was not the case some time ago. I suppose it needs a fix. Thanks.

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## [Blank spaces after segmentation](https://discourse.slicer.org/t/blank-spaces-after-segmentation/13201)

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**Author:** [@arifeuzundurukan](https://discourse.slicer.org/u/arifeuzundurukan)\
**Replies:** 5\
**Last updated:** [August 29, 2020, 2:39am UTC](https://discourse.slicer.org/t/blank-spaces-after-segmentation/13201 "2020-08-29T02:39:52Z")

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Hello everyone, I was trying to make segmentation of lungs and human soft tissue but after the segmentation I faced some blank spaces between the the lungs and human soft tissue. I would like to make a FEM analysis by …

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## [Normalisation of MR images](https://discourse.slicer.org/t/normalisation-of-mr-images/13215)

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**Author:** [@RadioQuest](https://discourse.slicer.org/u/RadioQuest)\
**Replies:** 0\
**Last updated:** [August 28, 2020, 3:55pm UTC](https://discourse.slicer.org/t/normalisation-of-mr-images/13215 "2020-08-28T15:55:24Z")

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Hi… I am working on MRI images from different sources and I want to compare the features. Is it possible to standardise primary diagnostic features (especially Original Image mean and maximum)? and does it have an effe…

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## [SlicerJupyter Extension](https://discourse.slicer.org/t/slicerjupyter-extension/13196)

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**Author:** [@Fereshte\_J](https://discourse.slicer.org/u/Fereshte_J)\
**Replies:** 2\
**Last updated:** [August 28, 2020, 3:51pm UTC](https://discourse.slicer.org/t/slicerjupyter-extension/13196 "2020-08-28T15:51:43Z")

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Problem report for Slicer 4.11.0-2020-08-26 win-amd64: \[please describe expected and actual behavior\] I want to install SlicerJupyter extension on slicer4.11 version 29320 however I cannot find the extension in the exte…

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## [Problem with extracting secondary features](https://discourse.slicer.org/t/problem-with-extracting-secondary-features/13214)

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**Author:** [@RadioQuest](https://discourse.slicer.org/u/RadioQuest)\
**Replies:** 0\
**Last updated:** [August 28, 2020, 3:50pm UTC](https://discourse.slicer.org/t/problem-with-extracting-secondary-features/13214 "2020-08-28T15:50:06Z")

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Hi… I am working on MRI data and for some of the ROI’s I got usual error. When extracted using PYradiomics - I received following 1.0 2.0 -3.20342650381492E-16 0.0 1.0 1.0 1.0 0.0 -3.20342650381492E-16 0.0 0…

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## [VMTK - Branch points coordinates](https://discourse.slicer.org/t/vmtk-branch-points-coordinates/13173)

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**Author:** [@janneke\_slicer](https://discourse.slicer.org/u/janneke_slicer)\
**Replies:** 2\
**Last updated:** [August 28, 2020, 9:26am UTC](https://discourse.slicer.org/t/vmtk-branch-points-coordinates/13173 "2020-08-28T09:26:19Z")

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Hello, I am using the VMTK extension in Slicer 4.11. It works really well; however, I would like to extract the branch point coordinates of the centerline model in a fast way. I know this is possible by creating the c…

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## [Fiducial spheres are distorted near the edge of 3D views in orthographic display](https://discourse.slicer.org/t/fiducial-spheres-are-distorted-near-the-edge-of-3d-views-in-orthographic-display/13198)

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**Author:** [@ungi](https://discourse.slicer.org/u/ungi)\
**Replies:** 4\
**Last updated:** [August 28, 2020, 3:30am UTC](https://discourse.slicer.org/t/fiducial-spheres-are-distorted-near-the-edge-of-3d-views-in-orthographic-display/13198 "2020-08-28T03:30:44Z")

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I just noticed an interesting optical feature. I’m not sure if this is a bug or normal. For context, I display CT images with volume rendering in orthographic mode. I need to zoom out a lot to see whole image. I noticed …

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## [How to measure minimun diameter?](https://discourse.slicer.org/t/how-to-measure-minimun-diameter/13080)

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**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\
**Replies:** 5\
**Last updated:** [August 28, 2020, 12:29am UTC](https://discourse.slicer.org/t/how-to-measure-minimun-diameter/13080 "2020-08-28T00:29:50Z")

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Hi everyone! Slicer version: 4.11.0-2020-07-04 r29204 Win I want to measure the minimun diameter of a pseudotube segment I´ve tryed Extract Centerline Module and Segment Statistics Module but I think radius dat…

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## [How to run segment editor python script from Terminal](https://discourse.slicer.org/t/how-to-run-segment-editor-python-script-from-terminal/13204)

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**Author:** [@epearlstone](https://discourse.slicer.org/u/epearlstone)\
**Replies:** 0\
**Last updated:** [August 27, 2020, 9:30pm UTC](https://discourse.slicer.org/t/how-to-run-segment-editor-python-script-from-terminal/13204 "2020-08-27T21:30:58Z")

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How can I run a python script from Terminal to create segmentation within slicer. I’ve read posts related to this but what my question boils down to is how to run the script itself from Terminal. Lets say I am using thi…

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## [Could not load...as a Scalar Volume](https://discourse.slicer.org/t/could-not-load-as-a-scalar-volume/13200)

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**Author:** [@sanna](https://discourse.slicer.org/u/sanna)\
**Replies:** 1\
**Last updated:** [August 27, 2020, 8:40pm UTC](https://discourse.slicer.org/t/could-not-load-as-a-scalar-volume/13200 "2020-08-27T20:40:15Z")

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Hi! I’ve just started using Slicer (I have an MRI scan of my spine that I’d like to export for 3D printing) and I’m stuck on the “Could not load…as a Scalar Volume”. I understand there can be several reasons for it, but …

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## [Get Centroid from Script](https://discourse.slicer.org/t/get-centroid-from-script/13191)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 2\
**Last updated:** [August 27, 2020, 6:05pm UTC](https://discourse.slicer.org/t/get-centroid-from-script/13191 "2020-08-27T18:05:27Z")

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I tried to get the centroid from obb\_centroid = np.array(stats\[segmentId,“LabelmapSegmentStatisticsPlugin.centroid\_ras”\]) but it gives KeyError. Can someone help me how to do that properly ? thanks

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## [Unit correct for my DICOM Data](https://discourse.slicer.org/t/unit-correct-for-my-dicom-data/13153)

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**Author:** [@Jini](https://discourse.slicer.org/u/Jini)\
**Replies:** 4\
**Last updated:** [August 26, 2020, 11:47am UTC](https://discourse.slicer.org/t/unit-correct-for-my-dicom-data/13153 "2020-08-26T11:47:06Z")

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Where can you calibrate or set the unit of the 3D slicer. By the segmentation and volume it shows me in mm, is this unit correct? Thanks

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## [Parametric skeleton model implementation in 3D Slicer](https://discourse.slicer.org/t/parametric-skeleton-model-implementation-in-3d-slicer/13160)

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**Author:** [@Cesar\_Puga](https://discourse.slicer.org/u/Cesar_Puga)\
**Replies:** 0\
**Last updated:** [August 25, 2020, 4:34pm UTC](https://discourse.slicer.org/t/parametric-skeleton-model-implementation-in-3d-slicer/13160 "2020-08-25T16:34:09Z")

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Dear Community, I am currently working on developing an application for performing needle insertion (for biopsy) with a robot arm, so far i have been able to setup and control the robot arm thanks to your help, the next…

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## [can not create midbrain surface mesh](https://discourse.slicer.org/t/can-not-create-midbrain-surface-mesh/13157)

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**Author:** [@Jacqueline\_Zhang](https://discourse.slicer.org/u/Jacqueline_Zhang)\
**Replies:** 1\
**Last updated:** [August 25, 2020, 1:33pm UTC](https://discourse.slicer.org/t/can-not-create-midbrain-surface-mesh/13157 "2020-08-25T13:33:33Z")

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Operating system: WIN 10 Slicer version: 4.8.1 Expected behavior: Create a mesh from freesurfer segmented data Actual behavior: error message: Model Maker standard error: Model scene file doesn’t exist yet: C:/Users/…

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## [research using Slicer software](https://discourse.slicer.org/t/research-using-slicer-software/13156)

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**Author:** [@samar\_adly](https://discourse.slicer.org/u/samar_adly)\
**Replies:** 0\
**Last updated:** [August 25, 2020, 1:20pm UTC](https://discourse.slicer.org/t/research-using-slicer-software/13156 "2020-08-25T13:20:50Z")

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Good evening, I am an assistant lecturer at faculty of dentistry, Orthodontics department, Alexandria University, Egypt. I am conducting a PhD research and i wanted. to use your software but i wanted to know what method …

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## [How to visualize 2d xray and 3d model overlapped](https://discourse.slicer.org/t/how-to-visualize-2d-xray-and-3d-model-overlapped/13142)

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**Author:** [@Henry\_Cope](https://discourse.slicer.org/u/Henry_Cope)\
**Replies:** 2\
**Last updated:** [August 24, 2020, 4:21pm UTC](https://discourse.slicer.org/t/how-to-visualize-2d-xray-and-3d-model-overlapped/13142 "2020-08-24T16:21:31Z")

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Hi all, Is it possible to visualize a 2D Xray in the same space as a 3D volume inside the 3D only viewer? I realize that from the start, it’s obvious that 2D will not appear in 3D. But is there any way to include it as …

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## [How to block the user selection of a node in a qMRMLNodeComboBox?](https://discourse.slicer.org/t/how-to-block-the-user-selection-of-a-node-in-a-qmrmlnodecombobox/11582)

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**Author:** [@xlucox](https://discourse.slicer.org/u/xlucox)\
**Replies:** 4\
**Last updated:** [August 24, 2020, 4:17pm UTC](https://discourse.slicer.org/t/how-to-block-the-user-selection-of-a-node-in-a-qmrmlnodecombobox/11582 "2020-08-24T16:17:05Z")

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Hello !!! I’m trying to prevent the user to select a node in a qMRMLNodeComboBox. I think it should be an object within this class to block the selection of nodes. I would appreciate if someone can help me. Thank you …

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## [Remeshing segmented model](https://discourse.slicer.org/t/remeshing-segmented-model/13141)

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**Author:** [@A\_Bonifacio](https://discourse.slicer.org/u/A_Bonifacio)\
**Replies:** 3\
**Last updated:** [August 24, 2020, 3:13pm UTC](https://discourse.slicer.org/t/remeshing-segmented-model/13141 "2020-08-24T15:13:42Z")

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Is it possible to remesh the surface of the segmented model specifying the element edge size (maybe using surface toolbox)? Thanks

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## [Issue creating binder repository to share Slicer notebooks (Wrong Kernel)](https://discourse.slicer.org/t/issue-creating-binder-repository-to-share-slicer-notebooks-wrong-kernel/13139)

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**Author:** [@allihuwa](https://discourse.slicer.org/u/allihuwa)\
**Replies:** 1\
**Last updated:** [August 24, 2020, 2:01pm UTC](https://discourse.slicer.org/t/issue-creating-binder-repository-to-share-slicer-notebooks-wrong-kernel/13139 "2020-08-24T14:01:15Z")

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Hello, I am trying to run my Github repository via binder to be able to share my slicer notebook files (.ipynb) with other people. I am able to create the binder repository but when I open up a .ipynb file the default k…

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## [Convert and export .stl file to .dcm](https://discourse.slicer.org/t/convert-and-export-stl-file-to-dcm/13093)

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**Author:** [@wjd582](https://discourse.slicer.org/u/wjd582)\
**Replies:** 17\
**Last updated:** [August 24, 2020, 1:27pm UTC](https://discourse.slicer.org/t/convert-and-export-stl-file-to-dcm/13093 "2020-08-24T13:27:50Z")

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Hi everyone, I would like to ask you to how to export the dicom file from .stl. I loaded .stl file (surface structure) and it had just outlier of the object. Is It possible to export as a dicom format? Thanks,

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## [Segment editor : specified terminology item in settings is partially taken into account](https://discourse.slicer.org/t/segment-editor-specified-terminology-item-in-settings-is-partially-taken-into-account/13114)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 3\
**Last updated:** [August 23, 2020, 3:55pm UTC](https://discourse.slicer.org/t/segment-editor-specified-terminology-item-in-settings-is-partially-taken-into-account/13114 "2020-08-23T15:55:34Z")

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‘Application settings / Segmentations’ section allows to define a default terminology entry when we add the first segment in ‘Segment editor’ module, or ‘Segmentations’ module. I select ‘Tissue/Artery’ there. After rest…

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## [Path explorer (Slicer IGT) does not save Trajectory](https://discourse.slicer.org/t/path-explorer-slicer-igt-does-not-save-trajectory/13132)

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**Author:** [@Michele\_Bailo](https://discourse.slicer.org/u/Michele_Bailo)\
**Replies:** 2\
**Last updated:** [August 23, 2020, 8:27am UTC](https://discourse.slicer.org/t/path-explorer-slicer-igt-does-not-save-trajectory/13132 "2020-08-23T08:27:33Z")

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OS: MacOS 10.15.6 and Windows 10 Slicer version:4.11.0-2020-08-15 Expected behavior: I find it extremely helpful and interesting to study trajectories with 3D slicer (e.g. for stereotactic procedures, research purposes…

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