# Latest

**URL:** https://discourse.slicer.org/latest.md?page=53

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

**Page:** 54

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## [Version 5.8.1 unable to use GetSegmentIdBySegmentName](https://discourse.slicer.org/t/version-5-8-1-unable-to-use-getsegmentidbysegmentname/43259)

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**Author:** [@maximeb](https://discourse.slicer.org/u/maximeb)\
**Replies:** 1\
**Last updated:** [June 8, 2025, 1:12am UTC](https://discourse.slicer.org/t/version-5-8-1-unable-to-use-getsegmentidbysegmentname/43259 "2025-06-08T01:12:48Z")

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Previously in version 5.6.2 this: self.SegmentID = Segmentation.GetSegmentIdBySegmentName(segment\_name) retrieved the segmentID In version 5.8.2, it returns none. Is that normal? What is the new equivalent for gettin…

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## [Tangent plane to a centerline](https://discourse.slicer.org/t/tangent-plane-to-a-centerline/20778)

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**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 7\
**Last updated:** [June 7, 2025, 3:06pm UTC](https://discourse.slicer.org/t/tangent-plane-to-a-centerline/20778 "2025-06-07T15:06:02Z")

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Is there any way to obtain planes tangent to a centerline? Thanks

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## [Dragging OsiriX xml file as segmentation to import into 3D slicer](https://discourse.slicer.org/t/dragging-osirix-xml-file-as-segmentation-to-import-into-3d-slicer/22031)

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**Author:** [@tenzin\_kunkyab](https://discourse.slicer.org/u/tenzin_kunkyab)\
**Replies:** 10\
**Last updated:** [June 7, 2025, 2:12pm UTC](https://discourse.slicer.org/t/dragging-osirix-xml-file-as-segmentation-to-import-into-3d-slicer/22031 "2025-06-07T14:12:32Z")

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I have a file with dicom images (CT volume) and xml as the segmentation (just one xml file), when I drag the whole file into the slicer, only dicom image is shown, I couldn’t get the xml segmentation to be imported. I c…

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## [Ignore or remove a Segment Editor undo state](https://discourse.slicer.org/t/ignore-or-remove-a-segment-editor-undo-state/43220)

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**Author:** [@mh00](https://discourse.slicer.org/u/mh00)\
**Replies:** 3\
**Last updated:** [June 6, 2025, 6:12pm UTC](https://discourse.slicer.org/t/ignore-or-remove-a-segment-editor-undo-state/43220 "2025-06-06T18:12:36Z")

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If I have a workflow like the following: Load CT and create a Segmentation Use Paint effect on red slice Use Paint effect on green slice Set a tag on the first segment of the segmentation node Use Paint effect on y…

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## [Issue with HDBrainExtraction Tool Not Completing – Error Message Appears](https://discourse.slicer.org/t/issue-with-hdbrainextraction-tool-not-completing-error-message-appears/43236)

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**Author:** [@MZA](https://discourse.slicer.org/u/MZA)\
**Replies:** 3\
**Last updated:** [June 7, 2025, 12:03am UTC](https://discourse.slicer.org/t/issue-with-hdbrainextraction-tool-not-completing-error-message-appears/43236 "2025-06-07T00:03:57Z")

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Hi everyone, I’m encountering an issue while using the HDBrainExtraction tool. After selecting the source and output volume and clicking Apply, the process fails to complete. Instead, I get the pop-up error message show…

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## [Project Week 43 Prep Meeting (June 10th)](https://discourse.slicer.org/t/project-week-43-prep-meeting-june-10th/43252)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [June 6, 2025, 6:09pm UTC](https://discourse.slicer.org/t/project-week-43-prep-meeting-june-10th/43252 "2025-06-06T18:09:55Z")

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Dear Project Week community, The next project week preparation meeting will be next Tuesday, June 10, at 10:00 AM ET. We will be discussing possible breakout sessions for the week (see Breakout Sessions for PW43). If …

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## [A  Cube  into segment](https://discourse.slicer.org/t/a-cube-into-segment/43218)

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**Author:** [@Farah\_BH](https://discourse.slicer.org/u/Farah_BH)\
**Replies:** 4\
**Last updated:** [June 6, 2025, 5:14pm UTC](https://discourse.slicer.org/t/a-cube-into-segment/43218 "2025-06-06T17:14:58Z")

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Hello,I created a markup ROI node ( a cube) on a ct volume, and now I want to convert it into a visible segment on that CT volume because I want to modify it. How to do so with the simplest approach?

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## [How to set dimensions and slice thickness when reconstructing FIB stack](https://discourse.slicer.org/t/how-to-set-dimensions-and-slice-thickness-when-reconstructing-fib-stack/43165)

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**Author:** [@Biaxialerzug](https://discourse.slicer.org/u/Biaxialerzug)\
**Replies:** 4\
**Last updated:** [June 6, 2025, 3:25pm UTC](https://discourse.slicer.org/t/how-to-set-dimensions-and-slice-thickness-when-reconstructing-fib-stack/43165 "2025-06-06T15:25:02Z")

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Hi, I’m using 3D Slicer to reconstruct a material volume. The slices of this volume were createt using FIB (Focused Ion Beam) in a SEM. At this point I struggle to set the correct dimensions of my volume. Each image of …

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## [Failed to compute results - Total Segmentator](https://discourse.slicer.org/t/failed-to-compute-results-total-segmentator/40062)

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**Author:** [@Guilherme\_Augusto](https://discourse.slicer.org/u/Guilherme_Augusto)\
**Replies:** 6\
**Last updated:** [June 6, 2025, 9:00am UTC](https://discourse.slicer.org/t/failed-to-compute-results-total-segmentator/40062 "2025-06-06T09:00:27Z")

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Hello, I am trying to use the TotalSegmentator module in Slicer 3D (version 5.7.0) for total body segmentation of a volume. However, when I click “Apply,” I receive the following error: Command ‘\[‘C:/Users/Drsti/AppDat…

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## [Estimating memory required for NNinteractive](https://discourse.slicer.org/t/estimating-memory-required-for-nninteractive/43239)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [June 5, 2025, 9:19pm UTC](https://discourse.slicer.org/t/estimating-memory-required-for-nninteractive/43239 "2025-06-05T21:19:02Z")

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Is there a way to predictably calculate the memory required to segment a volume using NNinteractive? For example given the 400x400x400 16 bit volume how much GPU memory would I need. I Trying to figure out via trial and…

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## [Code for TransformVisualizer?](https://discourse.slicer.org/t/code-for-transformvisualizer/43241)

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**Author:** [@elisedl1](https://discourse.slicer.org/u/elisedl1)\
**Replies:** 1\
**Last updated:** [June 5, 2025, 6:36pm UTC](https://discourse.slicer.org/t/code-for-transformvisualizer/43241 "2025-06-05T18:36:59Z")

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Hi all, Is there anyway to access the code for the TransformVisualizer module?

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## [Orientation marker not matching the view](https://discourse.slicer.org/t/orientation-marker-not-matching-the-view/43228)

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**Author:** [@Shirly\_Someck](https://discourse.slicer.org/u/Shirly_Someck)\
**Replies:** 1\
**Last updated:** [June 5, 2025, 4:58pm UTC](https://discourse.slicer.org/t/orientation-marker-not-matching-the-view/43228 "2025-06-05T16:58:57Z")

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Hi, I’m using slicer 5.6.2 on windows 10. I marked at the app settings patient right is screen right However, the orientation marker shows the other way: and the segmentation I loaded is also flipped. Is that a…

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## [Elastix not working](https://discourse.slicer.org/t/elastix-not-working/43205)

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**Author:** [@danielacpanciera](https://discourse.slicer.org/u/danielacpanciera)\
**Replies:** 1\
**Last updated:** [June 5, 2025, 3:26pm UTC](https://discourse.slicer.org/t/elastix-not-working/43205 "2025-06-05T15:26:26Z")

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Hi all, I recently installed Slicer 5.8.0 (and also 5.8.1) on my work’s laptop and I am having the following issue with Elastix since the update on Mon Mar 03 2025. \[Python\] Elastix primary method failed: module ‘Elast…

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## [Aligning local coordinate system with RAS](https://discourse.slicer.org/t/aligning-local-coordinate-system-with-ras/43230)

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**Author:** [@mariammtch](https://discourse.slicer.org/u/mariammtch)\
**Replies:** 1\
**Last updated:** [June 5, 2025, 2:29pm UTC](https://discourse.slicer.org/t/aligning-local-coordinate-system-with-ras/43230 "2025-06-05T14:29:58Z")

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Hello everyone. I have several CT scans which are all positioned differently. It is not important to align them with each other but it is very important for me that I use the local coordinate system for the measurements.…

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## [Extensions-manager](https://discourse.slicer.org/t/extensions-manager/43226)

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**Author:** [@zxy](https://discourse.slicer.org/u/zxy)\
**Replies:** 0\
**Last updated:** [June 5, 2025, 6:27am UTC](https://discourse.slicer.org/t/extensions-manager/43226 "2025-06-05T06:27:05Z")

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Why does the Bone Thickness Mapping extension in version 4.11 show the result as seen in the image after execution?

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## [I am currently facing an issue with the Elastix registration module in 3D Slicer ](https://discourse.slicer.org/t/i-am-currently-facing-an-issue-with-the-elastix-registration-module-in-3d-slicer/42217)

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**Author:** [@xiaoguan](https://discourse.slicer.org/u/xiaoguan)\
**Replies:** 2\
**Last updated:** [March 20, 2025, 11:16am UTC](https://discourse.slicer.org/t/i-am-currently-facing-an-issue-with-the-elastix-registration-module-in-3d-slicer/42217 "2025-03-20T11:16:12Z")

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Dear users of slicer, I hope this message finds you well. I am currently facing an issue with the Elastix registration module in 3D Slicer and would greatly appreciate your assistance in resolving it.The error log is be…

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## [How to convert xml file to RT Struct](https://discourse.slicer.org/t/how-to-convert-xml-file-to-rt-struct/43225)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 0\
**Last updated:** [June 5, 2025, 3:26am UTC](https://discourse.slicer.org/t/how-to-convert-xml-file-to-rt-struct/43225 "2025-06-05T03:26:24Z")

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Dear Expert, I have xml file (xml folder) that I done contouring on that file. The original file also I have as attached. Both file can get here: File XML and Original Anyone can help me to convert xml file to RT Stru…

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## [Segmentation of breast tumors](https://discourse.slicer.org/t/segmentation-of-breast-tumors/43181)

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**Author:** [@Meltem](https://discourse.slicer.org/u/Meltem)\
**Replies:** 2\
**Last updated:** [June 4, 2025, 5:35am UTC](https://discourse.slicer.org/t/segmentation-of-breast-tumors/43181 "2025-06-04T05:35:26Z")

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Hello, I am Meltem. New here. I have downloaded 3d Slicer 5.8.1. I have chosen the second phase of dynamic contrasted breas MRI to segment, and I want to segment the tumor via threshold (it’s a very complex tumor, manual…

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## [Error building custom 3D Slicer](https://discourse.slicer.org/t/error-building-custom-3d-slicer/43149)

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**Author:** [@nicofutur8](https://discourse.slicer.org/u/nicofutur8)\
**Replies:** 5\
**Last updated:** [June 4, 2025, 10:31am UTC](https://discourse.slicer.org/t/error-building-custom-3d-slicer/43149 "2025-06-04T10:31:04Z")

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Hello everyone! I want to build a custom Slicer3D using your template by Kitware. I followed steps thoroughly but, at the end of the building phase, i get an error envolving some kind of VTK feature called vtkTeemPython…

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## [How to package slicer to a zip for publication](https://discourse.slicer.org/t/how-to-package-slicer-to-a-zip-for-publication/43185)

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**Author:** [@zhaokaien](https://discourse.slicer.org/u/zhaokaien)\
**Replies:** 2\
**Last updated:** [June 4, 2025, 10:13am UTC](https://discourse.slicer.org/t/how-to-package-slicer-to-a-zip-for-publication/43185 "2025-06-04T10:13:01Z")

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Hello, I have successfully built Slicer v5.9 from source code, and Slicer runs normally. I’ve also performed custom development on Slicer, and everything works as expected. Now, I need to INSTALL and PACKAGE Slicer so we…

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## [Incorrect values when converting segmentation to binary labelmap](https://discourse.slicer.org/t/incorrect-values-when-converting-segmentation-to-binary-labelmap/43190)

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**Author:** [@JASON](https://discourse.slicer.org/u/JASON)\
**Replies:** 20\
**Last updated:** [June 3, 2025, 10:13pm UTC](https://discourse.slicer.org/t/incorrect-values-when-converting-segmentation-to-binary-labelmap/43190 "2025-06-03T22:13:00Z")

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I have noticed that converting a segmentation to binary labelmap causes all label values to be remapped from their current value to the segment’s index (1 … n+1). This is true for UI option “Export visible segments to b…

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## [HD-BET installation](https://discourse.slicer.org/t/hd-bet-installation/42727)

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**Author:** [@Claudia\_Takyi](https://discourse.slicer.org/u/Claudia_Takyi)\
**Replies:** 1\
**Last updated:** [June 3, 2025, 8:07pm UTC](https://discourse.slicer.org/t/hd-bet-installation/42727 "2025-06-03T20:07:04Z")

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Please, I am new to 3D Slicer. I am trying to use the HD-BET tool for a project but i can’t find it in the modules of my 3D Slicer application. Can anyone help me install this ?

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## [ALPACA (MALPACA) TUTORIAL: K-means\_templates\_selection](https://discourse.slicer.org/t/alpaca-malpaca-tutorial-k-means-templates-selection/43204)

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**Author:** [@Nicola\_Calcabrini](https://discourse.slicer.org/u/Nicola_Calcabrini)\
**Replies:** 1\
**Last updated:** [June 3, 2025, 2:37pm UTC](https://discourse.slicer.org/t/alpaca-malpaca-tutorial-k-means-templates-selection/43204 "2025-06-03T14:37:39Z")

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good morning, I’m trying the alpaca tutorial from this link: "https://github.com/chz31/Tutorials/blob/main/MALPACA/K-means\_templates\_selection.md " unfortunately I can’t get past the second step, I attach screenshot to …

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## [2025.05.27 Weekly Meeting](https://discourse.slicer.org/t/2025-05-27-weekly-meeting/43118)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [June 3, 2025, 2:00pm UTC](https://discourse.slicer.org/t/2025-05-27-weekly-meeting/43118 "2025-06-03T14:00:54Z")

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Today, we will be having our next weekly hangout at 11:00 AM ET until 12:00 PM ET, after the project week meeting. We will be reusing the Project Week Zoom link. Anyone is welcome to join at this link: Launch Meeting -…

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## [Preview builds not generated](https://discourse.slicer.org/t/preview-builds-not-generated/43201)

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**Author:** [@RafaelPalomar](https://discourse.slicer.org/u/RafaelPalomar)\
**Replies:** 0\
**Last updated:** [June 3, 2025, 9:17am UTC](https://discourse.slicer.org/t/preview-builds-not-generated/43201 "2025-06-03T09:17:04Z")

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Hello. The Slicer packages for Jun 02 don’t seem to have been generated. Is this expected? Many of the extensions, on the other hand, seem to be generated correctly.

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## [3D print CT of a skull without holes](https://discourse.slicer.org/t/3d-print-ct-of-a-skull-without-holes/43095)

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**Author:** [@hoteh](https://discourse.slicer.org/u/hoteh)\
**Replies:** 7\
**Last updated:** [June 3, 2025, 6:22am UTC](https://discourse.slicer.org/t/3d-print-ct-of-a-skull-without-holes/43095 "2025-06-03T06:22:22Z")

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I would like to 3D print a CT of a skull. The problem is, there are a lot of holes and islands in the scan. Is there any automatic tool to help? Other than manually filling the holes with “Paint” and removing the easy i…

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## [WM/GM/CSF Segmentation in FLAIR, T2\*, DWI, TOF Sequences](https://discourse.slicer.org/t/wm-gm-csf-segmentation-in-flair-t2-dwi-tof-sequences/43198)

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**Author:** [@m\_vanessa](https://discourse.slicer.org/u/m_vanessa)\
**Replies:** 0\
**Last updated:** [June 3, 2025, 5:18am UTC](https://discourse.slicer.org/t/wm-gm-csf-segmentation-in-flair-t2-dwi-tof-sequences/43198 "2025-06-03T05:18:02Z")

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Hi everyone, I’m looking for recommended methods or modules in 3D Slicer for segmenting white matter, gray matter, and CSF in MRI sequences like FLAIR, T2\*, DWI, and TOF . Are there tools or workflows that handle these…

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## [vBMD and automatic segmentation ](https://discourse.slicer.org/t/vbmd-and-automatic-segmentation/43197)

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**Author:** [@Nora14](https://discourse.slicer.org/u/Nora14)\
**Replies:** 0\
**Last updated:** [June 3, 2025, 5:17am UTC](https://discourse.slicer.org/t/vbmd-and-automatic-segmentation/43197 "2025-06-03T05:17:49Z")

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Hello, I am new to 3D Slicer and I need to segment the femoral neck and calculate the vBMD of the femur from CT, if possible that the regions of interest can be automatically selected. The goal is to compare the pre- an…

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## [SlicerVirtualReality](https://discourse.slicer.org/t/slicervirtualreality/43067)

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**Author:** [@JaredAmudeo](https://discourse.slicer.org/u/JaredAmudeo)\
**Replies:** 1\
**Last updated:** [June 2, 2025, 1:04pm UTC](https://discourse.slicer.org/t/slicervirtualreality/43067 "2025-06-02T13:04:40Z")

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Hello! Does anyone know how I can install the Slicer VR module? I’m currently using version 5.7.0-2024-09-03, and it doesn’t appear in the extensions manager. Should I update to the latest version, or is there a way to i…

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## [Best way to segment and view semi-circular canals from CT scan in 3D](https://discourse.slicer.org/t/best-way-to-segment-and-view-semi-circular-canals-from-ct-scan-in-3d/41004)

<div class="topic-metadata">

**Author:** [@Holdmybrain](https://discourse.slicer.org/u/Holdmybrain)\
**Replies:** 5\
**Last updated:** [June 2, 2025, 10:59am UTC](https://discourse.slicer.org/t/best-way-to-segment-and-view-semi-circular-canals-from-ct-scan-in-3d/41004 "2025-06-02T10:59:15Z")

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Hey guys and gals, I’m a patient with a keen interest in understanding and visualising scans better and have just started learning to use Slicer (on Macosx version 5.2.2). I’ve been playing around with creating basic r…

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