# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=175

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

**Page:** 176

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## [Extensions problem](https://discourse.slicer.org/t/extensions-problem/28206)

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**Author:** [@soukup.la](https://discourse.slicer.org/u/soukup.la)\
**Replies:** 3\
**Last updated:** [March 8, 2023, 6:54am UTC](https://discourse.slicer.org/t/extensions-problem/28206 "2023-03-08T06:54:57Z")

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Hello, I have problem with SurfaceWrapSolidify extensions. Could you help me please? OS: Ubuntu 22.04.2 LTS Slicer version 5.2.2

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## [How to create 3D volumes of segmented vessels from .mhd/.raw?](https://discourse.slicer.org/t/how-to-create-3d-volumes-of-segmented-vessels-from-mhd-raw/28225)

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**Author:** [@hoppymop](https://discourse.slicer.org/u/hoppymop)\
**Replies:** 3\
**Last updated:** [March 8, 2023, 6:42am UTC](https://discourse.slicer.org/t/how-to-create-3d-volumes-of-segmented-vessels-from-mhd-raw/28225 "2023-03-08T06:42:00Z")

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Hej, My aim is to create 3D volumes of .mhd/.raw-files of segmented abdomen vessels (CT-images) and eventually extract the center-lines. The 3D volume of the segmented vessels looks like this: There is one CT-data s…

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## [Nifti file and freesurfer pial file mismatch in slicer](https://discourse.slicer.org/t/nifti-file-and-freesurfer-pial-file-mismatch-in-slicer/11387)

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**Author:** [@Tutu](https://discourse.slicer.org/u/Tutu)\
**Replies:** 3\
**Last updated:** [March 8, 2023, 5:34am UTC](https://discourse.slicer.org/t/nifti-file-and-freesurfer-pial-file-mismatch-in-slicer/11387 "2023-03-08T05:34:07Z")

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Hi slicers, I tried to view several files that were built from Freesurfer (brain.mgz, l/rh.pial,l/rh.white). However, I found the surface of the pial could not match the outline of raw MRI images. I checked online and f…

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## [Image loaded from tiff stack appears distorted](https://discourse.slicer.org/t/image-loaded-from-tiff-stack-appears-distorted/28228)

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**Author:** [@studyskin](https://discourse.slicer.org/u/studyskin)\
**Replies:** 1\
**Last updated:** [March 8, 2023, 3:46am UTC](https://discourse.slicer.org/t/image-loaded-from-tiff-stack-appears-distorted/28228 "2023-03-08T03:46:51Z")

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hi, does anybody know how i can fix my models being loaded warped? ive tried loading it with slicermorph and normal , thank you to anyone who can help :slight\_smile:

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## [Question on saving](https://discourse.slicer.org/t/question-on-saving/28217)

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**Author:** [@bcolbert](https://discourse.slicer.org/u/bcolbert)\
**Replies:** 10\
**Last updated:** [March 7, 2023, 11:56pm UTC](https://discourse.slicer.org/t/question-on-saving/28217 "2023-03-07T23:56:40Z")

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I am segmenting structures in fish. Once segmented, I develop a model (ply) which I will eventually use in a multi-species analysis. Once structures are segmented, I have saved using both the MRB and from saving the indi…

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## [Exporting segmentation as dcm](https://discourse.slicer.org/t/exporting-segmentation-as-dcm/28168)

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**Author:** [@Nadya\_Shusharina](https://discourse.slicer.org/u/Nadya_Shusharina)\
**Replies:** 7\
**Last updated:** [March 7, 2023, 8:45pm UTC](https://discourse.slicer.org/t/exporting-segmentation-as-dcm/28168 "2023-03-07T20:45:39Z")

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Operating system: Windows 11 PRO Slicer version: 5.2.1 Expected behavior: Export created segmentation to the DICOM database Actual behavior: No export Hello, I am creating segmentation in Segment Editor and exportin…

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## [Interpreting the variability of calcium on contrast-enhanced CT](https://discourse.slicer.org/t/interpreting-the-variability-of-calcium-on-contrast-enhanced-ct/28226)

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**Author:** [@Silvia](https://discourse.slicer.org/u/Silvia)\
**Replies:** 0\
**Last updated:** [March 7, 2023, 5:38pm UTC](https://discourse.slicer.org/t/interpreting-the-variability-of-calcium-on-contrast-enhanced-ct/28226 "2023-03-07T17:38:24Z")

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Hello, I’m attempting to calculate the Agatston Score on CT images with contrast. According to the method, calcification is considered present when HU values exceed 130. However, in my images, calcification begins at a r…

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## [How to set random colors to all segments inside a segmentation?](https://discourse.slicer.org/t/how-to-set-random-colors-to-all-segments-inside-a-segmentation/28218)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 0\
**Last updated:** [March 7, 2023, 2:27pm UTC](https://discourse.slicer.org/t/how-to-set-random-colors-to-all-segments-inside-a-segmentation/28218 "2023-03-07T14:27:03Z")

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I would like to make easy to differentiate the segments that are next to each other. Thank you

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## [Can't upgrade open3d](https://discourse.slicer.org/t/cant-upgrade-open3d/25307)

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**Author:** [@b\_pei](https://discourse.slicer.org/u/b_pei)\
**Replies:** 5\
**Last updated:** [March 6, 2023, 11:58pm UTC](https://discourse.slicer.org/t/cant-upgrade-open3d/25307 "2023-03-06T23:58:53Z")

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Hi, When I first load ALPACA, it failed to upgrade and it hit “Error: please check the url of the open3d wheel in the script” . I have tried the version 5.0.3 and 5.1.0. My computer system is windows 11. I have searc…

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## [How to create this type of view of Fastsurfer segmented volume](https://discourse.slicer.org/t/how-to-create-this-type-of-view-of-fastsurfer-segmented-volume/28177)

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**Author:** [@mukund\_shah](https://discourse.slicer.org/u/mukund_shah)\
**Replies:** 1\
**Last updated:** [March 6, 2023, 8:34pm UTC](https://discourse.slicer.org/t/how-to-create-this-type-of-view-of-fastsurfer-segmented-volume/28177 "2023-03-06T20:34:30Z")

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I have Fastsurfer segmentation map(nifti format) of a T1 brain volume ,how do i create a view that looks like the image below.

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## [Extension manager icons not shown on Mac](https://discourse.slicer.org/t/extension-manager-icons-not-shown-on-mac/28101)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [March 6, 2023, 1:56pm UTC](https://discourse.slicer.org/t/extension-manager-icons-not-shown-on-mac/28101 "2023-03-06T13:56:21Z")

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For some extensions on Mac, the icons are not found and instead of the extension specific icon, the generic plug-in one is shown. This doesn’t seem to happen in Windows or Linux. Screenshot below is from v5.2.2.

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## [Editing Mouse Wheel Zoom Preference](https://discourse.slicer.org/t/editing-mouse-wheel-zoom-preference/28166)

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**Author:** [@S\_Motch\_Perrine](https://discourse.slicer.org/u/S_Motch_Perrine)\
**Replies:** 2\
**Last updated:** [March 6, 2023, 1:39pm UTC](https://discourse.slicer.org/t/editing-mouse-wheel-zoom-preference/28166 "2023-03-06T13:39:43Z")

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I want to change the default function of my mouse wheel for Zoom. It is “backwards” to what I am used to using in other software. I looked in Application Settings, but don’t see if it’s possible to swap the wheel roll di…

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## [Virtual Bronchoscopy](https://discourse.slicer.org/t/virtual-bronchoscopy/7468)

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**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 10\
**Last updated:** [March 6, 2023, 10:37am UTC](https://discourse.slicer.org/t/virtual-bronchoscopy/7468 "2023-03-06T10:37:53Z")

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Hi, This is my first post here. I really enjoy 3D Slicer. Was using the airway segmentation tool of the chest imaging suite to produce an airway model from a CT scan. Worked well. The endoscopy module, however, does n…

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## [No 'editor's function in 5.0](https://discourse.slicer.org/t/no-editors-function-in-5-0/27859)

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**Author:** [@Fumi](https://discourse.slicer.org/u/Fumi)\
**Replies:** 18\
**Last updated:** [March 6, 2023, 10:12am UTC](https://discourse.slicer.org/t/no-editors-function-in-5-0/27859 "2023-03-06T10:12:04Z")

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Operating system:Diffusion MRI Slicer version:5.0.3 Expected behavior:Editor module was in Slicer 4.0 Actual behavior:No botton corresponding ‘editor’ in modules.

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## [Why are the extension manager updates not up-to-date?](https://discourse.slicer.org/t/why-are-the-extension-manager-updates-not-up-to-date/28169)

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**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 17\
**Last updated:** [March 6, 2023, 6:18am UTC](https://discourse.slicer.org/t/why-are-the-extension-manager-updates-not-up-to-date/28169 "2023-03-06T06:18:33Z")

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After an update on a 3D Slicer cloud server with the extension manager, the Lung CT Analyzer extension is dated 20.2.2023 - a gap of one and a half weeks with many commits. How can I force an update?

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## [Conversion of step file from stl file](https://discourse.slicer.org/t/conversion-of-step-file-from-stl-file/28185)

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**Author:** [@Mable](https://discourse.slicer.org/u/Mable)\
**Replies:** 0\
**Last updated:** [March 6, 2023, 5:49am UTC](https://discourse.slicer.org/t/conversion-of-step-file-from-stl-file/28185 "2023-03-06T05:49:31Z")

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How to convert segmented stl file from 3D slicer to step file

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## [Elastix, why applying a transform on image does not produce same image as the generated output at registration time?](https://discourse.slicer.org/t/elastix-why-applying-a-transform-on-image-does-not-produce-same-image-as-the-generated-output-at-registration-time/28179)

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**Author:** [@S\_Arbabi](https://discourse.slicer.org/u/S_Arbabi)\
**Replies:** 1\
**Last updated:** [March 6, 2023, 4:13am UTC](https://discourse.slicer.org/t/elastix-why-applying-a-transform-on-image-does-not-produce-same-image-as-the-generated-output-at-registration-time/28179 "2023-03-06T04:13:37Z")

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Hi, I have two MR images (fixed, moving) and do the Elastix “rigid” registration in Slicer (5.0.2): after this process finishes, I have a generated (registered) moving image (called Volume\_7) and a transformation (c…

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## [Install external extension/module SlicerSupervisedSegmentation](https://discourse.slicer.org/t/install-external-extension-module-slicersupervisedsegmentation/9116)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 4\
**Last updated:** [March 6, 2023, 1:17am UTC](https://discourse.slicer.org/t/install-external-extension-module-slicersupervisedsegmentation/9116 "2023-03-06T01:17:00Z")

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Hello, I would like to use the Slicer Supervised Segmentation extension (https://github.com/chalupaDaniel/SlicerSupervisedSegmentation ), but I do not understand how to access it from Slicer. Does it need to be built fr…

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## [Data node display nodes not maintained when creating a sequence](https://discourse.slicer.org/t/data-node-display-nodes-not-maintained-when-creating-a-sequence/28146)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 14\
**Last updated:** [March 4, 2023, 10:17pm UTC](https://discourse.slicer.org/t/data-node-display-nodes-not-maintained-when-creating-a-sequence/28146 "2023-03-04T22:17:38Z")

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I’ve been having some issues creating a sequence where the display nodes of the given data nodes that I’m adding are not being maintained. I have a set of loaded 2D images where I have customized each of their display vo…

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## [Regarding Reconstruct 4D cine MRI](https://discourse.slicer.org/t/regarding-reconstruct-4d-cine-mri/28163)

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**Author:** [@ICUH](https://discourse.slicer.org/u/ICUH)\
**Replies:** 1\
**Last updated:** [March 4, 2023, 4:16am UTC](https://discourse.slicer.org/t/regarding-reconstruct-4d-cine-mri/28163 "2023-03-04T04:16:41Z")

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Hi. I have 2D Cine MRI images with 25 frames for 2ch/4ch/multiple SAX slices. I was trying to generate 4D cine from those images using Reconstruct 4D Cine MRI from Slicer Heart plug in. Each set of images are loaded a…

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## [Load multiple cardiac phases for segmentation/virtual reality](https://discourse.slicer.org/t/load-multiple-cardiac-phases-for-segmentation-virtual-reality/5214)

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**Author:** [@sarvpriya1985](https://discourse.slicer.org/u/sarvpriya1985)\
**Replies:** 25\
**Last updated:** [March 4, 2023, 4:09am UTC](https://discourse.slicer.org/t/load-multiple-cardiac-phases-for-segmentation-virtual-reality/5214 "2023-03-04T04:09:47Z")

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Operating system: windows 10 Slicer version: 4.10 Expected behavior: See cine motion of all phases in volume render/segmentation and then virtual reality Actual behavior: Not working Hello everyone, I read the prior…

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## [Apply transfer function to 2D slices](https://discourse.slicer.org/t/apply-transfer-function-to-2d-slices/28162)

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**Author:** [@Amin\_Nasim\_saravi](https://discourse.slicer.org/u/Amin_Nasim_saravi)\
**Replies:** 1\
**Last updated:** [March 4, 2023, 3:35am UTC](https://discourse.slicer.org/t/apply-transfer-function-to-2d-slices/28162 "2023-03-04T03:35:07Z")

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Hello, Is it possible to use the manually designed transfer function in the “Volume Rendering” section as a color map for 2D slices? I want to see a slice of the volume, but with the color mapping that I defined in the …

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## [No Mac extensions](https://discourse.slicer.org/t/no-mac-extensions/12918)

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**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 3\
**Last updated:** [March 3, 2023, 6:18pm UTC](https://discourse.slicer.org/t/no-mac-extensions/12918 "2023-03-03T18:18:33Z")

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The extensions for MacOS have not built for today’s preview version, will these be available later?

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## [Create a new window with multiple slice views](https://discourse.slicer.org/t/create-a-new-window-with-multiple-slice-views/28132)

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**Author:** [@rhodesdante](https://discourse.slicer.org/u/rhodesdante)\
**Replies:** 2\
**Last updated:** [March 3, 2023, 5:54pm UTC](https://discourse.slicer.org/t/create-a-new-window-with-multiple-slice-views/28132 "2023-03-03T17:54:38Z")

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Is it possible to create a new window with multiple slice views? This example shows how to create a single additional view, but I am attempting to create multiple additional views so I can display them on a separate moni…

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## [Volume cropping CT images using lung masks](https://discourse.slicer.org/t/volume-cropping-ct-images-using-lung-masks/28155)

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**Author:** [@Vahdane](https://discourse.slicer.org/u/Vahdane)\
**Replies:** 2\
**Last updated:** [March 3, 2023, 2:58pm UTC](https://discourse.slicer.org/t/volume-cropping-ct-images-using-lung-masks/28155 "2023-03-03T14:58:55Z")

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Hello, I want to crop the lung CT image to lobe subregions by using lung masks. I have the masks, however, as far as I know, we can only crop the image to a rectangular shape in the crop volume module. Thanks for your …

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## [HTC Vive Focus 3 controllers not visible](https://discourse.slicer.org/t/htc-vive-focus-3-controllers-not-visible/28158)

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**Author:** [@okhoma](https://discourse.slicer.org/u/okhoma)\
**Replies:** 0\
**Last updated:** [March 3, 2023, 2:43pm UTC](https://discourse.slicer.org/t/htc-vive-focus-3-controllers-not-visible/28158 "2023-03-03T14:43:33Z")

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Operating system: Windows 10 Slicer version: 4.11.20210226 Expected behavior: Controllers visible during VR session Actual behavior: Controllers not visible, but the ability to interact with the volume is present. He…

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## [Fcal Temporal calibration with live streaming data](https://discourse.slicer.org/t/fcal-temporal-calibration-with-live-streaming-data/28150)

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**Author:** [@Qianqian\_Cai](https://discourse.slicer.org/u/Qianqian_Cai)\
**Replies:** 0\
**Last updated:** [March 3, 2023, 6:14am UTC](https://discourse.slicer.org/t/fcal-temporal-calibration-with-live-streaming-data/28150 "2023-03-03T06:14:40Z")

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Hardware: OptiTrack for tracking Clarius probe for imaging In the example configuration file of the temporal calibration, the two datasets from the tracker and probe were recorded and provided to fcal as sequence file…

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## [How can I create 3D dcm file with 2d image?](https://discourse.slicer.org/t/how-can-i-create-3d-dcm-file-with-2d-image/28147)

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**Author:** [@annkyotou](https://discourse.slicer.org/u/annkyotou)\
**Replies:** 1\
**Last updated:** [March 3, 2023, 5:55am UTC](https://discourse.slicer.org/t/how-can-i-create-3d-dcm-file-with-2d-image/28147 "2023-03-03T05:55:22Z")

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Hi, everyone. I am from the field of civil engineering. I would like to create 3D continuous .dcm files from a series of 2d .tiff files. How should I do this? Are .dcm files only generated from specific devices (e.g. C…

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## [Retrieving statistics from RTSTRUCT and scalar volume - binary labelmap representation computation is very slow](https://discourse.slicer.org/t/retrieving-statistics-from-rtstruct-and-scalar-volume-binary-labelmap-representation-computation-is-very-slow/28100)

<div class="topic-metadata">

**Author:** [@Markb](https://discourse.slicer.org/u/Markb)\
**Replies:** 5\
**Last updated:** [March 2, 2023, 9:59pm UTC](https://discourse.slicer.org/t/retrieving-statistics-from-rtstruct-and-scalar-volume-binary-labelmap-representation-computation-is-very-slow/28100 "2023-03-02T21:59:23Z")

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Hi all. I have access to some data which consists of a CT dataset and an accompanying RTSTRUCT file. This loads fine in 3D slicer, and I’ve even used it to generate some masked data which I then use in some Monte Carlo s…

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## [Real-time 3D ultrasound volume reconstruction using SlicerIGT extension](https://discourse.slicer.org/t/real-time-3d-ultrasound-volume-reconstruction-using-slicerigt-extension/11197)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 19\
**Last updated:** [March 2, 2023, 8:59pm UTC](https://discourse.slicer.org/t/real-time-3d-ultrasound-volume-reconstruction-using-slicerigt-extension/11197 "2023-03-02T20:59:18Z")

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3D Slicer’s SlicerIGT extension allows live data acquisition from a wide range of medical imaging, position tracking, and other devices and visualize and process the data in real-time. We have recently implemented huge …

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