# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=220

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

**Page:** 221

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## [Extensions updates are not dispayed in the Stable](https://discourse.slicer.org/t/extensions-updates-are-not-dispayed-in-the-stable/23648)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 7\
**Last updated:** [June 9, 2022, 8:48am UTC](https://discourse.slicer.org/t/extensions-updates-are-not-dispayed-in-the-stable/23648 "2022-06-09T08:48:45Z")

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At this point,“check for updates” functionality of the extension manager in 5.0.2 stable is problematic. It doesn’t find the updates… There are a lot of warnings about https, but I don’t see an actual error: @jcfr "ht…

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## [3D volumetric reconstruction from 2D images with 6DOF information offline](https://discourse.slicer.org/t/3d-volumetric-reconstruction-from-2d-images-with-6dof-information-offline/23783)

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**Author:** [@RealBrandonChen](https://discourse.slicer.org/u/RealBrandonChen)\
**Replies:** 1\
**Last updated:** [June 9, 2022, 6:39am UTC](https://discourse.slicer.org/t/3d-volumetric-reconstruction-from-2d-images-with-6dof-information-offline/23783 "2022-06-09T06:39:25Z")

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Hello, Does anyone know if I can reconstruct a 3D volumetric image with 2D images, of which the world coordinates and the rotation matrix (yaw, pitch, and row) are known? I want to do something like what SlicerIGT does, …

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## [Segmentation cannot be hidden](https://discourse.slicer.org/t/segmentation-cannot-be-hidden/23776)

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**Author:** [@jacobier](https://discourse.slicer.org/u/jacobier)\
**Replies:** 3\
**Last updated:** [June 9, 2022, 3:30am UTC](https://discourse.slicer.org/t/segmentation-cannot-be-hidden/23776 "2022-06-09T03:30:04Z")

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Is it a bug? Why my segmentations cannot be hidden even I click the eye icons?

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## [Visualization of Aorta thickness](https://discourse.slicer.org/t/visualization-of-aorta-thickness/23773)

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**Author:** [@dbgraf20](https://discourse.slicer.org/u/dbgraf20)\
**Replies:** 1\
**Last updated:** [June 8, 2022, 6:19pm UTC](https://discourse.slicer.org/t/visualization-of-aorta-thickness/23773 "2022-06-08T18:19:01Z")

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I need to segment the aortic wall. We are working with CT images. Is there a filter that I can apply to the images to enhance the CT images to show the vasculature? I just need some recommendations that way I don’t have …

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## [Segmentation on Rotated Data (or should we stick with axial,coronal,saggital planes?)](https://discourse.slicer.org/t/segmentation-on-rotated-data-or-should-we-stick-with-axial-coronal-saggital-planes/23766)

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**Author:** [@joosicky](https://discourse.slicer.org/u/joosicky)\
**Replies:** 2\
**Last updated:** [June 8, 2022, 4:33pm UTC](https://discourse.slicer.org/t/segmentation-on-rotated-data-or-should-we-stick-with-axial-coronal-saggital-planes/23766 "2022-06-08T16:33:33Z")

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Hello there. We are new at 3dslicer and we just trying to annotate some of our MRI datas, using 3dslicer segmentation tools. We have completed 1 of our data with fully manual segmentation. But in the end we have discove…

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## [Can vertex colored models be imported as segmentations?](https://discourse.slicer.org/t/can-vertex-colored-models-be-imported-as-segmentations/23761)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [June 8, 2022, 2:47pm UTC](https://discourse.slicer.org/t/can-vertex-colored-models-be-imported-as-segmentations/23761 "2022-06-08T14:47:25Z")

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See an example of vertex colored skull from MorphoSource. https://www.morphosource.org/concern/parent/000101191/media/000358488 These were derived from CT scans, which are also available on M/S, but the segmentations ar…

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## [Registration of two DICOM-Sets from MRI](https://discourse.slicer.org/t/registration-of-two-dicom-sets-from-mri/23475)

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**Author:** [@Leon\_Dosendepp](https://discourse.slicer.org/u/Leon_Dosendepp)\
**Replies:** 2\
**Last updated:** [June 8, 2022, 11:47am UTC](https://discourse.slicer.org/t/registration-of-two-dicom-sets-from-mri/23475 "2022-06-08T11:47:11Z")

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Operating system: Windows 10 Slicer version: 4.11.20210226 Expected behavior: Two DICOM-Sets of different size are registered with landmark registration and one DICOM-Set with both combined is exported. Actual behavio…

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## [How to merge MRI and brain atlas](https://discourse.slicer.org/t/how-to-merge-mri-and-brain-atlas/5288)

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**Author:** [@flashman](https://discourse.slicer.org/u/flashman)\
**Replies:** 3\
**Last updated:** [January 7, 2019, 6:16am UTC](https://discourse.slicer.org/t/how-to-merge-mri-and-brain-atlas/5288 "2019-01-07T06:16:34Z")

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Operating system: Windows 10 Slicer version: 4.10 Hi all, I am relatively new to the 3D Slicer program and currently undergoing the precise localization of electrodes after deep brain stimulation (DBS) surgery. I’ve…

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## [.bmp slowing segmentation down and changing scaling of micro-CT images?](https://discourse.slicer.org/t/bmp-slowing-segmentation-down-and-changing-scaling-of-micro-ct-images/23758)

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**Author:** [@dbgraf20](https://discourse.slicer.org/u/dbgraf20)\
**Replies:** 2\
**Last updated:** [June 7, 2022, 8:32pm UTC](https://discourse.slicer.org/t/bmp-slowing-segmentation-down-and-changing-scaling-of-micro-ct-images/23758 "2022-06-07T20:32:25Z")

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We have a micro-CT scanner that will only spit out .bmp files for us. My entire 3d slicer career I have only used .dcm. Segmentation has been nearly instant with .dcm files. My question comes from the fact that slicer do…

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## [Capture 3D view into PNG file with transparent background not working as expected](https://discourse.slicer.org/t/capture-3d-view-into-png-file-with-transparent-background-not-working-as-expected/23740)

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**Author:** [@aliabidi](https://discourse.slicer.org/u/aliabidi)\
**Replies:** 4\
**Last updated:** [June 7, 2022, 12:54pm UTC](https://discourse.slicer.org/t/capture-3d-view-into-png-file-with-transparent-background-not-working-as-expected/23740 "2022-06-07T12:54:14Z")

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I have a 3D image which I want to take a screenshot of, I do not want to have the background or the axes (I, R, S) or purple lines when I save the image. The current state looks as follows: I have run the ‘Capture 3D…

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## [Why the two fiducial points have the same value?](https://discourse.slicer.org/t/why-the-two-fiducial-points-have-the-same-value/23711)

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**Author:** [@MAXFAXSURGEON](https://discourse.slicer.org/u/MAXFAXSURGEON)\
**Replies:** 3\
**Last updated:** [June 7, 2022, 12:49pm UTC](https://discourse.slicer.org/t/why-the-two-fiducial-points-have-the-same-value/23711 "2022-06-07T12:49:24Z")

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Dears in 3D Slicer support team, I am using 4.11.2021.02.26 version and after doing Pick’n paint, model to model distance, and mesh statistics for measuring the distance different of two different time CT created surfac…

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## [Can't remember Slicer based app running on web](https://discourse.slicer.org/t/cant-remember-slicer-based-app-running-on-web/23751)

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**Author:** [@keri](https://discourse.slicer.org/u/keri)\
**Replies:** 2\
**Last updated:** [June 7, 2022, 12:19pm UTC](https://discourse.slicer.org/t/cant-remember-slicer-based-app-running-on-web/23751 "2022-06-07T12:19:50Z")

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Hi, I remember I accidently stumbled on Slicer based application that was running on WEB and it used to have dark style with beatiful blue colors. I think it used something different from Qt, probably C# or javascript. …

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## [Python script for threshold based Bone segmentation](https://discourse.slicer.org/t/python-script-for-threshold-based-bone-segmentation/23752)

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**Author:** [@gzt036](https://discourse.slicer.org/u/gzt036)\
**Replies:** 1\
**Last updated:** [June 7, 2022, 12:03pm UTC](https://discourse.slicer.org/t/python-script-for-threshold-based-bone-segmentation/23752 "2022-06-07T12:03:49Z")

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Is there a python script or function to run threshold based segmentation for Bones after the DICOM file is loaded into slicer? Thanks.

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## [How to use linear transform to convert X,Y Coordinate to RAS coordinates](https://discourse.slicer.org/t/how-to-use-linear-transform-to-convert-x-y-coordinate-to-ras-coordinates/23735)

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**Author:** [@minhtan16](https://discourse.slicer.org/u/minhtan16)\
**Replies:** 1\
**Last updated:** [June 7, 2022, 10:43am UTC](https://discourse.slicer.org/t/how-to-use-linear-transform-to-convert-x-y-coordinate-to-ras-coordinates/23735 "2022-06-07T10:43:22Z")

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Hi everyone, I have multiples 2D coordinates (X,Y). These coordinates are all mapped by a linear transform in which I have access. I’m wondering if there’s a way to convert a 2D coordinates using the linear transform ma…

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## [Slicer crashes when using segment editor](https://discourse.slicer.org/t/slicer-crashes-when-using-segment-editor/23664)

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**Author:** [@cin\_zh\_ao](https://discourse.slicer.org/u/cin_zh_ao)\
**Replies:** 3\
**Last updated:** [June 7, 2022, 10:30am UTC](https://discourse.slicer.org/t/slicer-crashes-when-using-segment-editor/23664 "2022-06-07T10:30:22Z")

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I have just downloaded the 5.0.2 version of 3D Slicer on my Macbook and it keeps malfunctioning. Whenever I try to use the scissor tool in Segment Editor, the application crashes after a few minutes and erases all of my …

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## [\[Linux\] Opening extension manager makes slicer stuck](https://discourse.slicer.org/t/linux-opening-extension-manager-makes-slicer-stuck/23651)

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**Author:** [@SaraPoli22](https://discourse.slicer.org/u/SaraPoli22)\
**Replies:** 6\
**Last updated:** [June 7, 2022, 9:34am UTC](https://discourse.slicer.org/t/linux-opening-extension-manager-makes-slicer-stuck/23651 "2022-06-07T09:34:13Z")

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Hi, I’m working with Slicer 5.0.2 on Linux, but when I try to open extension manager the program crashes. I looked at the topic Opening extension manager makes Slicer crash on Linux, but couldn’t find a solution that wo…

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## [Structures segmented in either Arterial/Venous phases are slightly misaligned when switching view to the other phase](https://discourse.slicer.org/t/structures-segmented-in-either-arterial-venous-phases-are-slightly-misaligned-when-switching-view-to-the-other-phase/23748)

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**Author:** [@rjk](https://discourse.slicer.org/u/rjk)\
**Replies:** 3\
**Last updated:** [June 7, 2022, 9:02am UTC](https://discourse.slicer.org/t/structures-segmented-in-either-arterial-venous-phases-are-slightly-misaligned-when-switching-view-to-the-other-phase/23748 "2022-06-07T09:02:13Z")

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Operating system: macOS 12.3.1 Slicer version: 5.0.2 Expected behavior: arterial+ venous phases align perfectly Actual behavior: slight offset between structures between A and V phases, e.g., a structure segmented in …

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## [Slicer kernel died when importing cv2](https://discourse.slicer.org/t/slicer-kernel-died-when-importing-cv2/23745)

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**Author:** [@user4](https://discourse.slicer.org/u/user4)\
**Replies:** 1\
**Last updated:** [June 7, 2022, 8:58am UTC](https://discourse.slicer.org/t/slicer-kernel-died-when-importing-cv2/23745 "2022-06-07T08:58:50Z")

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Hi,all.I want to use opencv so I installed it. However,when I import cv2,it takes a long time and failed in the end, as follows: I tried a lot of times ,it is still the same result…It only fails when I select Slic…

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## [Methods used in creating axial and sagittal in 3d Slicer](https://discourse.slicer.org/t/methods-used-in-creating-axial-and-sagittal-in-3d-slicer/23730)

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**Author:** [@Gabriela\_Zurliana](https://discourse.slicer.org/u/Gabriela_Zurliana)\
**Replies:** 2\
**Last updated:** [June 6, 2022, 8:29pm UTC](https://discourse.slicer.org/t/methods-used-in-creating-axial-and-sagittal-in-3d-slicer/23730 "2022-06-06T20:29:18Z")

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Hello! pardon for any mistakes I made here, this is my first time posting a question in this forum. I am currently trying to create a segmentation of the spine from a self-gathered data using ultrasound and is trying to…

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## [Unable to load DICOM segmentation - missing slice thickness](https://discourse.slicer.org/t/unable-to-load-dicom-segmentation-missing-slice-thickness/23737)

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**Author:** [@koeglfryderyk](https://discourse.slicer.org/u/koeglfryderyk)\
**Replies:** 2\
**Last updated:** [June 6, 2022, 4:52pm UTC](https://discourse.slicer.org/t/unable-to-load-dicom-segmentation-missing-slice-thickness/23737 "2022-06-06T16:52:46Z")

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I’m unable to load a DICOM segmentation. The segmentation was created by the Brainlab Curve navigation system in the AMIGO suite. I unfortunately cannot share the file. Tested on the latest preview version (version 5.…

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## [Saving content of .3dus file to .nnrd and .seq.nrrd files without using Slicer.exe window](https://discourse.slicer.org/t/saving-content-of-3dus-file-to-nnrd-and-seq-nrrd-files-without-using-slicer-exe-window/23732)

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**Author:** [@zurg](https://discourse.slicer.org/u/zurg)\
**Replies:** 0\
**Last updated:** [June 6, 2022, 12:31pm UTC](https://discourse.slicer.org/t/saving-content-of-3dus-file-to-nnrd-and-seq-nrrd-files-without-using-slicer-exe-window/23732 "2022-06-06T12:31:08Z")

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Hi all, I’d like to save the content of the .3dus file (as with “3D ultrasound image” description in Slicer) to the .nrrd and .seq.nrrd files, by using Slicer functionality but without opening the Slicer.exe window. Can…

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## [How to download offline zip install file of LanguagePacks? Because I can't search out or find it in 3DSlicer 4.11 extension manager](https://discourse.slicer.org/t/how-to-download-offline-zip-install-file-of-languagepacks-because-i-cant-search-out-or-find-it-in-3dslicer-4-11-extension-manager/23712)

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**Author:** [@Unicom](https://discourse.slicer.org/u/Unicom)\
**Replies:** 2\
**Last updated:** [June 6, 2022, 11:10am UTC](https://discourse.slicer.org/t/how-to-download-offline-zip-install-file-of-languagepacks-because-i-cant-search-out-or-find-it-in-3dslicer-4-11-extension-manager/23712 "2022-06-06T11:10:21Z")

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How to download offline zip install file of LanguagePacks? Because I can’t search out or find it in 3DSlicer 4.11 extension manager. OS：windows 10 LTSC 21H2 slicer version：4.11

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## [Pipeline for measuring surface area & issues with dynamic modeller](https://discourse.slicer.org/t/pipeline-for-measuring-surface-area-issues-with-dynamic-modeller/23725)

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**Author:** [@sridhar](https://discourse.slicer.org/u/sridhar)\
**Replies:** 0\
**Last updated:** [June 6, 2022, 8:55am UTC](https://discourse.slicer.org/t/pipeline-for-measuring-surface-area-issues-with-dynamic-modeller/23725 "2022-06-06T08:55:44Z")

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Hello, I was hoping someone could provide me feedback on the pipeline I am developing for measuring the eye surface area of insects (from microCT scans) and figure out the specific issue I am having when performing surf…

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## [How to load dense DVFs (from VoxelMorph) to Slicer](https://discourse.slicer.org/t/how-to-load-dense-dvfs-from-voxelmorph-to-slicer/23705)

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**Author:** [@BraveDistribution](https://discourse.slicer.org/u/BraveDistribution)\
**Replies:** 11\
**Last updated:** [June 6, 2022, 8:01am UTC](https://discourse.slicer.org/t/how-to-load-dense-dvfs-from-voxelmorph-to-slicer/23705 "2022-06-06T08:01:22Z")

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Hello, I have my whole pipeline implemented in Slicer (sequence registration (elastix) and application to surface models). I have ~20 patients and 2k volumes per patient (liver displacement due to respiratory cycle), wh…

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## [Bugs in Log Messages module](https://discourse.slicer.org/t/bugs-in-log-messages-module/23721)

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**Author:** [@gzt036](https://discourse.slicer.org/u/gzt036)\
**Replies:** 0\
**Last updated:** [June 6, 2022, 1:30am UTC](https://discourse.slicer.org/t/bugs-in-log-messages-module/23721 "2022-06-06T01:30:08Z")

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Operating system: windows Slicer version: 5.1.0 Expected behavior: Actual behavior: If I just click “errors” , I see picture 1 I can only see ‘picture 2’ if I first click “messages”, then click “errors”, Someth…

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## [Knee MRI Segmentation: Efficiency](https://discourse.slicer.org/t/knee-mri-segmentation-efficiency/23713)

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**Author:** [@Abdulla\_Al\_Shibli](https://discourse.slicer.org/u/Abdulla_Al_Shibli)\
**Replies:** 1\
**Last updated:** [June 5, 2022, 2:44pm UTC](https://discourse.slicer.org/t/knee-mri-segmentation-efficiency/23713 "2022-06-05T14:44:06Z")

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Hi, I am currently segmenting the bones (Femur, Tibia, Patella, etc.), ligaments, and tendons of a knee MRI. Pasted is a screenshot of what it looks like. I’m currently just painting and using the fill between slices fu…

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## [MONAI label does not utilize Tesala GPU](https://discourse.slicer.org/t/monai-label-does-not-utilize-tesala-gpu/23695)

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**Author:** [@Ron](https://discourse.slicer.org/u/Ron)\
**Replies:** 5\
**Last updated:** [June 5, 2022, 1:00pm UTC](https://discourse.slicer.org/t/monai-label-does-not-utilize-tesala-gpu/23695 "2022-06-05T13:00:05Z")

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I have been working with Andres to train a MONAI label spine segmentation on a windows 10 pro workstation (Lenovo p610, 64 core CPU AMD Threadripper pro, Nvidia Tesla V100, Quadro 1000 GPU, 256Gb Ram). We have tried sev…

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## [Scale the whole segmentation](https://discourse.slicer.org/t/scale-the-whole-segmentation/15902)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 19\
**Last updated:** [June 5, 2022, 11:08am UTC](https://discourse.slicer.org/t/scale-the-whole-segmentation/15902 "2022-06-05T11:08:59Z")

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Hello, How can we scale up/down a whole segmentation? I want to do it in segment editor by changing the size of the main volume, but it seems that my RAM is not enough for that. I am wondering whether there is a way to…

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## [open3D not installing when opening ALPACA for the first time](https://discourse.slicer.org/t/open3d-not-installing-when-opening-alpaca-for-the-first-time/22779)

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**Author:** [@Erik.Meilak](https://discourse.slicer.org/u/Erik.Meilak)\
**Replies:** 17\
**Last updated:** [June 4, 2022, 9:12am UTC](https://discourse.slicer.org/t/open3d-not-installing-when-opening-alpaca-for-the-first-time/22779 "2022-06-04T09:12:23Z")

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I have Slicer 4.11.20210226 on Windows 10. When trying to use ALPACA for the first time, the software attempts to upgrade open3d however never manages to. I am met with the following errors. Requirement already satisfie…

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## [Converting DICOM to NRRD on Docker via a Python script](https://discourse.slicer.org/t/converting-dicom-to-nrrd-on-docker-via-a-python-script/21096)

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**Author:** [@adouv](https://discourse.slicer.org/u/adouv)\
**Replies:** 7\
**Last updated:** [June 3, 2022, 12:18pm UTC](https://discourse.slicer.org/t/converting-dicom-to-nrrd-on-docker-via-a-python-script/21096 "2022-06-03T12:18:11Z")

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Hello, I would like to start off thanking all of you for the great work with 3D Slicer. It is truly a phenomenal piece of software! The issue we are having requires some description, so I will split this question into tw…

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