# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=261

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

**Page:** 262

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## [Smooth Mesh? Comparison to MATLAB](https://discourse.slicer.org/t/smooth-mesh-comparison-to-matlab/19616)

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**Author:** [@JoJo](https://discourse.slicer.org/u/JoJo)\
**Replies:** 2\
**Last updated:** [September 10, 2021, 7:02pm UTC](https://discourse.slicer.org/t/smooth-mesh-comparison-to-matlab/19616 "2021-09-10T19:02:41Z")

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Hello, for my bachelor thesis I segmented a bone out CT volume data via MATLAB and exported it with stlwrite. For a comparison I’ve used 3D Slicer too. Now I noticed that the 3D-Slicer mesh is much more smoother than th…

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## [Any way to move segmentations to match the newly registered volumes?](https://discourse.slicer.org/t/any-way-to-move-segmentations-to-match-the-newly-registered-volumes/19611)

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**Author:** [@akshay\_pillai](https://discourse.slicer.org/u/akshay_pillai)\
**Replies:** 3\
**Last updated:** [September 10, 2021, 5:13pm UTC](https://discourse.slicer.org/t/any-way-to-move-segmentations-to-match-the-newly-registered-volumes/19611 "2021-09-10T17:13:25Z")

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I don’t know if this is possible but if it is please let me know - I created segmentations with multiple segments using 2 volumes. But I later registered or aligned the two volumes to overlap. Now I need to move the segm…

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## [Landmarking on Volume Rendering Only?](https://discourse.slicer.org/t/landmarking-on-volume-rendering-only/19610)

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**Author:** [@ebryson](https://discourse.slicer.org/u/ebryson)\
**Replies:** 2\
**Last updated:** [September 10, 2021, 4:36pm UTC](https://discourse.slicer.org/t/landmarking-on-volume-rendering-only/19610 "2021-09-10T16:36:41Z")

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Hi, A few colleagues have asked me if they have to make a model before they add landmarks, or if they can just load the volume, bring up the volume rending and start placing landmarks. The program allows you to do that …

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## [Create line profile for given coordinates not markup points](https://discourse.slicer.org/t/create-line-profile-for-given-coordinates-not-markup-points/19586)

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**Author:** [@M.Odaba](https://discourse.slicer.org/u/M.Odaba)\
**Replies:** 3\
**Last updated:** [September 10, 2021, 3:16am UTC](https://discourse.slicer.org/t/create-line-profile-for-given-coordinates-not-markup-points/19586 "2021-09-10T03:16:14Z")

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I went through the Python code of the Line Profile, it only accepts the location of markup points manually created on the views to create a line profile. I need to create the line profiles out of know coordinates in the …

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## [Grouped markups display control](https://discourse.slicer.org/t/grouped-markups-display-control/19579)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 7\
**Last updated:** [September 10, 2021, 3:12am UTC](https://discourse.slicer.org/t/grouped-markups-display-control/19579 "2021-09-10T03:12:31Z")

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Often, I need to visualize a group of markups together for comparison and need I way to control their display properties jointly via UI. If we are to take on this, what would be the more straightforward way of implement…

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## [Need to segment a hole](https://discourse.slicer.org/t/need-to-segment-a-hole/19445)

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**Author:** [@jordanan](https://discourse.slicer.org/u/jordanan)\
**Replies:** 11\
**Last updated:** [September 9, 2021, 6:19pm UTC](https://discourse.slicer.org/t/need-to-segment-a-hole/19445 "2021-09-09T18:19:06Z")

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I would like to segment a hole in a bone. Having no luck with thresholding is there another way that can allow me to do this quickly? Thanks

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## [Negative Values in DVF Histogram](https://discourse.slicer.org/t/negative-values-in-dvf-histogram/19008)

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**Author:** [@toyama](https://discourse.slicer.org/u/toyama)\
**Replies:** 35\
**Last updated:** [September 9, 2021, 8:31am UTC](https://discourse.slicer.org/t/negative-values-in-dvf-histogram/19008 "2021-09-09T08:31:18Z")

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We are looking for a histogram of the DVF. The DVF should not have any negative values, but when I calculated the histogram from the DVF created by the transform module, it took negative values. What do these negative …

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## [The result of segmentation looks flat](https://discourse.slicer.org/t/the-result-of-segmentation-looks-flat/19535)

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**Author:** [@Damir\_G](https://discourse.slicer.org/u/Damir_G)\
**Replies:** 3\
**Last updated:** [September 9, 2021, 12:05pm UTC](https://discourse.slicer.org/t/the-result-of-segmentation-looks-flat/19535 "2021-09-09T12:05:14Z")

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Hello, I am working with CT scan images of a permafrost core. I am using 3D Slicer to get a 3D model of constituents. I.e. I have a stack of images and certain threshold values and I use “Segment Editor” in 3D Slicer. O…

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## [Segment editor has disappeared from the screen](https://discourse.slicer.org/t/segment-editor-has-disappeared-from-the-screen/19350)

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**Author:** [@11122](https://discourse.slicer.org/u/11122)\
**Replies:** 10\
**Last updated:** [August 27, 2021, 12:49pm UTC](https://discourse.slicer.org/t/segment-editor-has-disappeared-from-the-screen/19350 "2021-08-27T12:49:45Z")

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The 3DSlicer segmentation editor has disappeared from the screen, but if you know how to return it, please let me know. I also tried uninstalling it, but it will remain gone even if I re-download it. (translated …

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## [Margin effect to dilate segmentation](https://discourse.slicer.org/t/margin-effect-to-dilate-segmentation/19565)

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**Author:** [@Mgi](https://discourse.slicer.org/u/Mgi)\
**Replies:** 4\
**Last updated:** [September 9, 2021, 1:14am UTC](https://discourse.slicer.org/t/margin-effect-to-dilate-segmentation/19565 "2021-09-09T01:14:39Z")

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Hi everyone, I’m using 3d slicer, 4.11.20200930 version on windows 10. When I use the Margin effect tool to dilate a segmentation I defined a margin size of 1.01 mm. However, below it appears “Actual: 0.5 x 0.5 x 1.0 mm…

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## [Improving/Troubleshooting alignment in ALPACA?](https://discourse.slicer.org/t/improving-troubleshooting-alignment-in-alpaca/19582)

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**Author:** [@rsulser](https://discourse.slicer.org/u/rsulser)\
**Replies:** 4\
**Last updated:** [September 8, 2021, 9:39pm UTC](https://discourse.slicer.org/t/improving-troubleshooting-alignment-in-alpaca/19582 "2021-09-08T21:39:23Z")

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Operating system: Windows 10 (20H2) Slicer version: 4.11.20210226 Expected behavior: Alignment and orientation of models prior to ALPACA landmarking Actual behavior: Models orient but do not appear to align Hello all…

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## [Segment statistics from each slice](https://discourse.slicer.org/t/segment-statistics-from-each-slice/19569)

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**Author:** [@melindamareesmith](https://discourse.slicer.org/u/melindamareesmith)\
**Replies:** 2\
**Last updated:** [September 8, 2021, 9:04pm UTC](https://discourse.slicer.org/t/segment-statistics-from-each-slice/19569 "2021-09-08T21:04:41Z")

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Hello, I can see how to extract mean scalar value for a segment from the segment statistics, but what I would like to do is extract this for each MRI slice- in a similar way to how the segment cross-sectional area outpu…

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## [Filling between slices in oblique reformat slices](https://discourse.slicer.org/t/filling-between-slices-in-oblique-reformat-slices/19584)

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**Author:** [@hagop\_hovaguimian](https://discourse.slicer.org/u/hagop_hovaguimian)\
**Replies:** 2\
**Last updated:** [September 8, 2021, 8:29pm UTC](https://discourse.slicer.org/t/filling-between-slices-in-oblique-reformat-slices/19584 "2021-09-08T20:29:12Z")

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Hi Guys, Unable to get fill between slices when slices are created on a reformatted volume. Is there a way to do it? would be very helpful. Help!

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## [How to adjust the distorted image?](https://discourse.slicer.org/t/how-to-adjust-the-distorted-image/817)

<div class="topic-metadata">

**Author:** [@doc-xie](https://discourse.slicer.org/u/doc-xie)\
**Replies:** 87\
**Last updated:** [September 8, 2021, 6:05pm UTC](https://discourse.slicer.org/t/how-to-adjust-the-distorted-image/817 "2021-09-08T18:05:07Z")

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Hi! After the data was loaded into 3D Slicer,the axinal and coronal view display normally,but the saggital view was distored. I cannot understand the reason about this problem,furthermore,whether it is possible the pro…

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## [Unable to manually install extension to manual Slicer build](https://discourse.slicer.org/t/unable-to-manually-install-extension-to-manual-slicer-build/19359)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 9\
**Last updated:** [September 8, 2021, 4:35pm UTC](https://discourse.slicer.org/t/unable-to-manually-install-extension-to-manual-slicer-build/19359 "2021-09-08T16:35:25Z")

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I have built latest Slicer manually and have also built some Slicer extensions manually to install into the extension manager by ZIP. I’m running into an issue where they are being detected as incorrect matching revisio…

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## [Compare upper jaw teeth before and after orthodontic treatment](https://discourse.slicer.org/t/compare-upper-jaw-teeth-before-and-after-orthodontic-treatment/18608)

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**Author:** [@Nikhil\_Jain](https://discourse.slicer.org/u/Nikhil_Jain)\
**Replies:** 11\
**Last updated:** [September 8, 2021, 2:22pm UTC](https://discourse.slicer.org/t/compare-upper-jaw-teeth-before-and-after-orthodontic-treatment/18608 "2021-09-08T14:22:46Z")

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how to overlap 2 volumes to observe changes using fixed landmarks? (the two volumes being 3d stl files of upper jaw teeth before and after orthodontic treatment) Operating system:Windows 10 Slicer version:4.13 Expecte…

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## [How to obtain Coordinates of the Bounding Box](https://discourse.slicer.org/t/how-to-obtain-coordinates-of-the-bounding-box/19553)

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**Author:** [@Rituraj\_Dutta](https://discourse.slicer.org/u/Rituraj_Dutta)\
**Replies:** 5\
**Last updated:** [September 8, 2021, 2:16pm UTC](https://discourse.slicer.org/t/how-to-obtain-coordinates-of-the-bounding-box/19553 "2021-09-08T14:16:20Z")

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I have generated a bounding box (cuboid) for the liver in 3d Slicer using the ROI tool. How can I get the coordinates of the cuboid ?

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## [Mirror brain CT](https://discourse.slicer.org/t/mirror-brain-ct/19545)

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**Author:** [@bartvandijken](https://discourse.slicer.org/u/bartvandijken)\
**Replies:** 3\
**Last updated:** [September 8, 2021, 2:14pm UTC](https://discourse.slicer.org/t/mirror-brain-ct/19545 "2021-09-08T14:14:33Z")

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Operating system: MacOS Slicer version: 4.8.1 I’m trying to create a mean radiotherapy dose map on a cohort of 12 brain tumor patients with dose accumulation and isodose lines using the RT extension. However, I first w…

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## [Obtain the HU values for given 3D points with x,y,z coordinates](https://discourse.slicer.org/t/obtain-the-hu-values-for-given-3d-points-with-x-y-z-coordinates/19478)

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**Author:** [@M.Odaba](https://discourse.slicer.org/u/M.Odaba)\
**Replies:** 2\
**Last updated:** [September 8, 2021, 10:19am UTC](https://discourse.slicer.org/t/obtain-the-hu-values-for-given-3d-points-with-x-y-z-coordinates/19478 "2021-09-08T10:19:00Z")

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Hi, I’ve been trying to find a way to obtain the HU values for specific x,y,z coordinates. I explain what I’m trying to do. Let say I have a CT scan of a bone and I have generated rays in 3D space. Once these rays inte…

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## [How to scale up and down an object imported from STL ?](https://discourse.slicer.org/t/how-to-scale-up-and-down-an-object-imported-from-stl/19517)

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**Author:** [@mdear](https://discourse.slicer.org/u/mdear)\
**Replies:** 3\
**Last updated:** [September 8, 2021, 4:02am UTC](https://discourse.slicer.org/t/how-to-scale-up-and-down-an-object-imported-from-stl/19517 "2021-09-08T04:02:28Z")

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I am using a David SLS-1 scanner to produce an STL file of a small smooth opaque white tubular medical object (tracheostomy tube). When I take measurements inside slicer I notice there are some scaling issues. I have fi…

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## [Hyphen/dash in CLI command long flag argument](https://discourse.slicer.org/t/hyphen-dash-in-cli-command-long-flag-argument/19526)

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**Author:** [@benzwick](https://discourse.slicer.org/u/benzwick)\
**Replies:** 6\
**Last updated:** [September 8, 2021, 3:57am UTC](https://discourse.slicer.org/t/hyphen-dash-in-cli-command-long-flag-argument/19526 "2021-09-08T03:57:07Z")

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I am developing a Python CLI module for some software that uses hyphens in command line arguments. I created the XML file and loaded everything into 3D Slicer but I get the following error due to the hyphen/dash in the l…

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## [Spine Vertebra Instance Segmentation](https://discourse.slicer.org/t/spine-vertebra-instance-segmentation/19423)

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**Author:** [@oguzcanbekar](https://discourse.slicer.org/u/oguzcanbekar)\
**Replies:** 4\
**Last updated:** [September 8, 2021, 2:26am UTC](https://discourse.slicer.org/t/spine-vertebra-instance-segmentation/19423 "2021-09-08T02:26:58Z")

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Hello everyone, I’m a graduate student and working on medical images. Nowadays I am trying to segment my CT Spine data as instance segmentation. I tried to use 3D Slicer for this purpose, but I encountered many problems.…

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## [How to import two stl, superimpose and get volume differences](https://discourse.slicer.org/t/how-to-import-two-stl-superimpose-and-get-volume-differences/14262)

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**Author:** [@bharat](https://discourse.slicer.org/u/bharat)\
**Replies:** 1\
**Last updated:** [September 7, 2021, 10:03pm UTC](https://discourse.slicer.org/t/how-to-import-two-stl-superimpose-and-get-volume-differences/14262 "2021-09-07T22:03:09Z")

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

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## [SlicerJupiter extension not found](https://discourse.slicer.org/t/slicerjupiter-extension-not-found/16434)

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**Author:** [@dalbenzioG](https://discourse.slicer.org/u/dalbenzioG)\
**Replies:** 1\
**Last updated:** [September 7, 2021, 7:38pm UTC](https://discourse.slicer.org/t/slicerjupiter-extension-not-found/16434 "2021-09-07T19:38:59Z")

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Hello everyone, I have downloaded the latest stable version 4.11.20210226 and I try to install the SlicerJupiter extension from the Extention Manager. My current operating system is Ubuntu 20.04.1 LTS. I tried the sear…

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## [Open 3d slicer application with qtcreator](https://discourse.slicer.org/t/open-3d-slicer-application-with-qtcreator/19429)

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**Author:** [@xianger-qi](https://discourse.slicer.org/u/xianger-qi)\
**Replies:** 1\
**Last updated:** [September 7, 2021, 7:33pm UTC](https://discourse.slicer.org/t/open-3d-slicer-application-with-qtcreator/19429 "2021-09-07T19:33:09Z")

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There are some problems about opening 3d slicer with qt creator version 4.9.0 in linux. I preform the instructions following C++ debugging with Qt Creator — 3D Slicer documentation. problem 1: when i execute the comman…

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## [How to interact with module using python interactor? / is there a scripting info box?](https://discourse.slicer.org/t/how-to-interact-with-module-using-python-interactor-is-there-a-scripting-info-box/17990)

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**Author:** [@mgpoirot](https://discourse.slicer.org/u/mgpoirot)\
**Replies:** 1\
**Last updated:** [September 7, 2021, 7:07pm UTC](https://discourse.slicer.org/t/how-to-interact-with-module-using-python-interactor-is-there-a-scripting-info-box/17990 "2021-09-07T19:07:48Z")

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I’ve been able to load a file by drag and dropping it into slicer. The GUI pops up and an extension (SlicerFreeSurfer) recognizes its format and the file can be loaded. How would I replace the same actions using the co…

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## [I have a coordinate transformation matrix, but it seems not right when i apply it to the coordinate model in the transform module](https://discourse.slicer.org/t/i-have-a-coordinate-transformation-matrix-but-it-seems-not-right-when-i-apply-it-to-the-coordinate-model-in-the-transform-module/17963)

<div class="topic-metadata">

**Author:** [@yulaomao](https://discourse.slicer.org/u/yulaomao)\
**Replies:** 1\
**Last updated:** [September 7, 2021, 7:03pm UTC](https://discourse.slicer.org/t/i-have-a-coordinate-transformation-matrix-but-it-seems-not-right-when-i-apply-it-to-the-coordinate-model-in-the-transform-module/17963 "2021-09-07T19:03:20Z")

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The original coordinate system is the world coordinate system, and the new coordinate system takes the center of two balls as the Y axis. I use Python to do linear transform for a coordinate system shape model, and it wo…

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## [How to use CMF registration](https://discourse.slicer.org/t/how-to-use-cmf-registration/17379)

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**Author:** [@lili-yu22](https://discourse.slicer.org/u/lili-yu22)\
**Replies:** 1\
**Last updated:** [September 7, 2021, 7:01pm UTC](https://discourse.slicer.org/t/how-to-use-cmf-registration/17379 "2021-09-07T19:01:26Z")

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please look at the photo，what is the problem?

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## [STL file import, edit and volume measurment](https://discourse.slicer.org/t/stl-file-import-edit-and-volume-measurment/17377)

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**Author:** [@ashkansh](https://discourse.slicer.org/u/ashkansh)\
**Replies:** 1\
**Last updated:** [September 7, 2021, 6:59pm UTC](https://discourse.slicer.org/t/stl-file-import-edit-and-volume-measurment/17377 "2021-09-07T18:59:23Z")

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Hi all, I imported a .STL file as segmentation and I tried to cut a piece of the part and measure the volume of the rest. When I tried to use segment editor to use scissors, I had to define the volume as I defined it i…

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## [Export as a separate DICOM series the sagittal reconstruction, from axial DICOM series](https://discourse.slicer.org/t/export-as-a-separate-dicom-series-the-sagittal-reconstruction-from-axial-dicom-series/11514)

<div class="topic-metadata">

**Author:** [@Klaas](https://discourse.slicer.org/u/Klaas)\
**Replies:** 2\
**Last updated:** [September 7, 2021, 5:39pm UTC](https://discourse.slicer.org/t/export-as-a-separate-dicom-series-the-sagittal-reconstruction-from-axial-dicom-series/11514 "2021-09-07T17:39:57Z")

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Operating system: Win 10 Slicer version: 4.10.2 Expected behavior: I’m a novice to the tool, please help on how one can export as a separate DICOM series the sagittal/coronal reconstruction, from axial DICOM series. Th…

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