# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=56

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

**Page:** 57

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## [Nasal Build and Reconsturction; 3D CT and 3D MRI to show bone and soft tissue interaction.](https://discourse.slicer.org/t/nasal-build-and-reconsturction-3d-ct-and-3d-mri-to-show-bone-and-soft-tissue-interaction/41173)

<div class="topic-metadata">

**Author:** [@Justin\_Rhiner](https://discourse.slicer.org/u/Justin_Rhiner)\
**Replies:** 7\
**Last updated:** [January 22, 2025, 8:06am UTC](https://discourse.slicer.org/t/nasal-build-and-reconsturction-3d-ct-and-3d-mri-to-show-bone-and-soft-tissue-interaction/41173 "2025-01-22T08:06:29Z")

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Hello I am trying to reconstruct and show every piece of nasal septum, cartilidge and bone in a nose like. I currently have a 64 slice nasal CT and a nasal MRI. I have been able to rebuild the CT and show the crooked na…

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## [Activate Fill in mode](https://discourse.slicer.org/t/activate-fill-in-mode/41204)

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**Author:** [@mbol](https://discourse.slicer.org/u/mbol)\
**Replies:** 1\
**Last updated:** [January 22, 2025, 2:24am UTC](https://discourse.slicer.org/t/activate-fill-in-mode/41204 "2025-01-22T02:24:11Z")

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Hello everyone! I just simply want to activate the fill in mode on segmentation editor. I want to be able to draw a circle and get it filled automatically. I looked everywhere for instructions which all brinigng up Tool…

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## [Lost data of segmentation](https://discourse.slicer.org/t/lost-data-of-segmentation/41201)

<div class="topic-metadata">

**Author:** [@yuvaraj\_bigwigs](https://discourse.slicer.org/u/yuvaraj_bigwigs)\
**Replies:** 1\
**Last updated:** [January 22, 2025, 2:19am UTC](https://discourse.slicer.org/t/lost-data-of-segmentation/41201 "2025-01-22T02:19:21Z")

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Hi guys I am new to slicer tool. I did segmentation using segmentation option in slicer and I accidentally saved it as .nhrd file Instead of .nrrd file.if I try loading the .nhrd file it show Cannot load file.What shoul…

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## [Spectral Lung CT. Ventilation and perfusión](https://discourse.slicer.org/t/spectral-lung-ct-ventilation-and-perfusion/41191)

<div class="topic-metadata">

**Author:** [@titotitoide](https://discourse.slicer.org/u/titotitoide)\
**Replies:** 0\
**Last updated:** [January 21, 2025, 2:06pm UTC](https://discourse.slicer.org/t/spectral-lung-ct-ventilation-and-perfusion/41191 "2025-01-21T14:06:38Z")

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Hi I am trying to analyze a lung CT scan I have performed to assess the perfusion ventilation of a patient. I have performed it using a spectral CT. Is there any way to obtain a perfusion ventilation map using 3D slice? …

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## [Cannot see slice view](https://discourse.slicer.org/t/cannot-see-slice-view/41142)

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**Author:** [@coenwang01](https://discourse.slicer.org/u/coenwang01)\
**Replies:** 5\
**Last updated:** [January 21, 2025, 1:34pm UTC](https://discourse.slicer.org/t/cannot-see-slice-view/41142 "2025-01-21T13:34:37Z")

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I want to set three points to form a slice, then cut models with it. Therefore, I referred to this script. All the operations I performed are as follows: I dropped 3 markups control points in the scene and copy-paste the…

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## [AssertionError in distutils while installing Torch with PytorchUtils for Segment Anything Model-based extension](https://discourse.slicer.org/t/assertionerror-in-distutils-while-installing-torch-with-pytorchutils-for-segment-anything-model-based-extension/41167)

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**Author:** [@oothomas](https://discourse.slicer.org/u/oothomas)\
**Replies:** 1\
**Last updated:** [January 20, 2025, 4:38pm UTC](https://discourse.slicer.org/t/assertionerror-in-distutils-while-installing-torch-with-pytorchutils-for-segment-anything-model-based-extension/41167 "2025-01-20T16:38:22Z")

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I’m developing an extension called SlicerPhotogrammetry that uses Meta’s Segment Anything model. Because Segment Anything requires PyTorch (and thus Torch + TorchVision), I’m programmatically installing PyTorch inside th…

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## [Slicer 4.10.2 Crashing](https://discourse.slicer.org/t/slicer-4-10-2-crashing/41163)

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**Author:** [@ValerieS](https://discourse.slicer.org/u/ValerieS)\
**Replies:** 1\
**Last updated:** [January 20, 2025, 2:57pm UTC](https://discourse.slicer.org/t/slicer-4-10-2-crashing/41163 "2025-01-20T14:57:40Z")

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Operating system: Windows Slicer version: 4.10.2 Expected behavior: To be able to use the software Actual behavior: Slicer keeps crashing when using. I haven’t used this software for quite some time, so thought I wou…

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## [Can we edit multiple segments at once?](https://discourse.slicer.org/t/can-we-edit-multiple-segments-at-once/41101)

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**Author:** [@Dr\_Akshaya\_S\_R1](https://discourse.slicer.org/u/Dr_Akshaya_S_R1)\
**Replies:** 7\
**Last updated:** [January 20, 2025, 2:51pm UTC](https://discourse.slicer.org/t/can-we-edit-multiple-segments-at-once/41101 "2025-01-20T14:51:28Z")

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Im working on a oroject that involves more than 35 to 40 segments and each representing anatomy with similar threshold. So im thinking on working on them simultaneously. Is that possible?

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## [Surface area of adjacent segments](https://discourse.slicer.org/t/surface-area-of-adjacent-segments/41166)

<div class="topic-metadata">

**Author:** [@amreen\_spsingh](https://discourse.slicer.org/u/amreen_spsingh)\
**Replies:** 1\
**Last updated:** [January 20, 2025, 2:04pm UTC](https://discourse.slicer.org/t/surface-area-of-adjacent-segments/41166 "2025-01-20T14:04:54Z")

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I am currently working on paranasal sinuses which may be filled with polypoidal mucosa in the diseased state. So I have created two separate segmentations inside the sinuses… One containing air (green) and the other cont…

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## [Importing 2D-time series ](https://discourse.slicer.org/t/importing-2d-time-series/41164)

<div class="topic-metadata">

**Author:** [@dehnjo54](https://discourse.slicer.org/u/dehnjo54)\
**Replies:** 1\
**Last updated:** [January 20, 2025, 2:03pm UTC](https://discourse.slicer.org/t/importing-2d-time-series/41164 "2025-01-20T14:03:10Z")

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Hello, I am new to 3D Slicer and want to work on Segmentation of 2D-time-Series. I have multiple Dicom Studies where the same slice is captured in CT at multiple (\>100) time steps, varying from 60s to 3s per step. When …

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## [Why can not use dental segmentator?](https://discourse.slicer.org/t/why-can-not-use-dental-segmentator/40866)

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**Author:** [@Moh\_d\_Al-Watary](https://discourse.slicer.org/u/Moh_d_Al-Watary)\
**Replies:** 4\
**Last updated:** [January 20, 2025, 11:18am UTC](https://discourse.slicer.org/t/why-can-not-use-dental-segmentator/40866 "2025-01-20T11:18:48Z")

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Dears, wish you are doing fine and happy new year to all. I have added the module “dental segmentator” to 3D Slicer 5.7 and when trying to used it the program ask to download the needed extension “NNUNet and PyTorch” w…

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## [3d cube after python crop](https://discourse.slicer.org/t/3d-cube-after-python-crop/41154)

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**Author:** [@Andras\_Gomori](https://discourse.slicer.org/u/Andras_Gomori)\
**Replies:** 2\
**Last updated:** [January 20, 2025, 10:24am UTC](https://discourse.slicer.org/t/3d-cube-after-python-crop/41154 "2025-01-20T10:24:20Z")

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I’m working in win 10 with slicer, and in wsl. I’m using nifti files, and try to crop them. I use simple ITK for this purpose. The crop (somewhat) works, in the 2d views it is great. But in the 3d view the 3d cube work…

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## [rib cartilage segmentation](https://discourse.slicer.org/t/rib-cartilage-segmentation/40252)

<div class="topic-metadata">

**Author:** [@Vanessa](https://discourse.slicer.org/u/Vanessa)\
**Replies:** 2\
**Last updated:** [January 20, 2025, 8:39am UTC](https://discourse.slicer.org/t/rib-cartilage-segmentation/40252 "2025-01-20T08:39:25Z")

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How can I do the segmentation of the rib cartilage and measure the volume of the 7th and 8th rib cartilage? I need the volume to measure the degree of calcification for a study.

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## [How to align NIfTI files with original DICOM files?](https://discourse.slicer.org/t/how-to-align-nifti-files-with-original-dicom-files/41107)

<div class="topic-metadata">

**Author:** [@oi\_o](https://discourse.slicer.org/u/oi_o)\
**Replies:** 4\
**Last updated:** [January 20, 2025, 4:49am UTC](https://discourse.slicer.org/t/how-to-align-nifti-files-with-original-dicom-files/41107 "2025-01-20T04:49:35Z")

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I encountered an issue while trying to align NIfTI files (segmentation results from TotalSegmentator) with the original DICOM files in Jupyter Notebook. Despite my efforts to construct an appropriate affine matrix for th…

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## [Looking for Public Cardiac Ultrasound Volumes](https://discourse.slicer.org/t/looking-for-public-cardiac-ultrasound-volumes/41103)

<div class="topic-metadata">

**Author:** [@Hanae](https://discourse.slicer.org/u/Hanae)\
**Replies:** 2\
**Last updated:** [January 20, 2025, 12:56am UTC](https://discourse.slicer.org/t/looking-for-public-cardiac-ultrasound-volumes/41103 "2025-01-20T00:56:57Z")

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Hello, I’m currently exploring how reinforcement learning can be applied to autonomous ultrasound scanning. As part of my research, I’m looking for publicly available 3D volumes of cardiac ultrasound that I can use in 3…

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## [Multiple volume renderings are not displayed correctly](https://discourse.slicer.org/t/multiple-volume-renderings-are-not-displayed-correctly/41147)

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**Author:** [@Stuart](https://discourse.slicer.org/u/Stuart)\
**Replies:** 4\
**Last updated:** [January 19, 2025, 10:05pm UTC](https://discourse.slicer.org/t/multiple-volume-renderings-are-not-displayed-correctly/41147 "2025-01-19T22:05:06Z")

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My goal is to use the transforms editor to align two different volume renderings of the same skull, each rendered in a different color. No matter how I change the orientations, the gold version of the skull always shows …

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## [Paint with round brush](https://discourse.slicer.org/t/paint-with-round-brush/41153)

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**Author:** [@Tobias\_Koffer](https://discourse.slicer.org/u/Tobias_Koffer)\
**Replies:** 1\
**Last updated:** [January 19, 2025, 1:30pm UTC](https://discourse.slicer.org/t/paint-with-round-brush/41153 "2025-01-19T13:30:07Z")

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Hi, I have to segment a laryngeal tumor, but the paint function doesnt work on the tumor tissue, in other words, it doesnt recognize the tissue? Is there a better tool for tumor segmentation in that area? Thank you

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## [MONAI Auto3DSeg inference sources](https://discourse.slicer.org/t/monai-auto3dseg-inference-sources/36929)

<div class="topic-metadata">

**Author:** [@wesselk](https://discourse.slicer.org/u/wesselk)\
**Replies:** 1\
**Last updated:** [June 21, 2024, 7:32pm UTC](https://discourse.slicer.org/t/monai-auto3dseg-inference-sources/36929 "2024-06-21T19:32:37Z")

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Hi all, I have been working with the new MONAI Auto3DSeg and have a few questions if someone could help me out: 1- Where can I find the source for the models used? For example, “Madiastinal anatomy TS2” is not in MONA…

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## [How to align two models (stl) and then do landmarks on it? ](https://discourse.slicer.org/t/how-to-align-two-models-stl-and-then-do-landmarks-on-it/39589)

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**Author:** [@Puja\_Ghosh](https://discourse.slicer.org/u/Puja_Ghosh)\
**Replies:** 5\
**Last updated:** [January 17, 2025, 10:02pm UTC](https://discourse.slicer.org/t/how-to-align-two-models-stl-and-then-do-landmarks-on-it/39589 "2025-01-17T22:02:01Z")

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I have two models(stl) of torso (pregnant) and I am trying to align them one after another (superimpose) and then I want to do landmarks on the specific points where there are electrodes placed (checking position of elec…

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## [Segment Editor Sphere Brush](https://discourse.slicer.org/t/segment-editor-sphere-brush/41108)

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**Author:** [@tighek](https://discourse.slicer.org/u/tighek)\
**Replies:** 3\
**Last updated:** [January 17, 2025, 8:31pm UTC](https://discourse.slicer.org/t/segment-editor-sphere-brush/41108 "2025-01-17T20:31:00Z")

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Operating system: Windows 11 Slicer version: Slicer 5.6.2 Expected behavior: In “Segment Editor, Erase, Sphere Brush, Edit in 3D views”, the Sphere Brush is silver while erasing. Actual behavior: The silver Sphere Bru…

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## [Extracting point cloud data and occupancy map](https://discourse.slicer.org/t/extracting-point-cloud-data-and-occupancy-map/41127)

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**Author:** [@Jeednya\_Sade](https://discourse.slicer.org/u/Jeednya_Sade)\
**Replies:** 0\
**Last updated:** [January 17, 2025, 12:05pm UTC](https://discourse.slicer.org/t/extracting-point-cloud-data-and-occupancy-map/41127 "2025-01-17T12:05:41Z")

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Hi there, I need to extract the point cloud data and occupancy map for a 3D model which I get after segmentation. I guess there is a way to get point cloud as numpy array but how do I go about the occupancy map?

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## [Is it possible to create an effect to operate on closed surface objects?](https://discourse.slicer.org/t/is-it-possible-to-create-an-effect-to-operate-on-closed-surface-objects/41122)

<div class="topic-metadata">

**Author:** [@coenwang01](https://discourse.slicer.org/u/coenwang01)\
**Replies:** 0\
**Last updated:** [January 17, 2025, 8:10am UTC](https://discourse.slicer.org/t/is-it-possible-to-create-an-effect-to-operate-on-closed-surface-objects/41122 "2025-01-17T08:10:57Z")

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So far, all existing effects seem to be able to operate only on binary labelmap objects. Is it possible to create an effect to operate directly on closed surface objects? If so, could give me some suggestions? I’d be ver…

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## [Error when saving .nrrd files](https://discourse.slicer.org/t/error-when-saving-nrrd-files/41119)

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**Author:** [@Willa\_Coultley](https://discourse.slicer.org/u/Willa_Coultley)\
**Replies:** 1\
**Last updated:** [January 16, 2025, 9:08pm UTC](https://discourse.slicer.org/t/error-when-saving-nrrd-files/41119 "2025-01-16T21:08:03Z")

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Os - Mac sequoia 15 Slicer version - most current File types - Dicom loaded Expected behavior - saving volume renders in the .nrrd file format Actual behavior - receiving error status only on the volume renders that …

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## [Version 5.6.2 cerebral vasculature segmentation from MR](https://discourse.slicer.org/t/version-5-6-2-cerebral-vasculature-segmentation-from-mr/41118)

<div class="topic-metadata">

**Author:** [@BDhoth](https://discourse.slicer.org/u/BDhoth)\
**Replies:** 0\
**Last updated:** [January 16, 2025, 6:28pm UTC](https://discourse.slicer.org/t/version-5-6-2-cerebral-vasculature-segmentation-from-mr/41118 "2025-01-16T18:28:40Z")

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What is the most efficient way to segment small cerebral vasculature with 5.6.2?

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## [No windows/linux extension for preview in Cdash](https://discourse.slicer.org/t/no-windows-linux-extension-for-preview-in-cdash/41117)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 0\
**Last updated:** [January 16, 2025, 6:23pm UTC](https://discourse.slicer.org/t/no-windows-linux-extension-for-preview-in-cdash/41117 "2025-01-16T18:23:26Z")

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No sure why, only Mac ones are listed. @jcfr @Sam\_Horvath

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## [TotalSegmentator Failed to compute results....returned non-zero exit status 1](https://discourse.slicer.org/t/totalsegmentator-failed-to-compute-results-returned-non-zero-exit-status-1/38142)

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**Author:** [@yk\_Chen](https://discourse.slicer.org/u/yk_Chen)\
**Replies:** 10\
**Last updated:** [January 16, 2025, 2:04pm UTC](https://discourse.slicer.org/t/totalsegmentator-failed-to-compute-results-returned-non-zero-exit-status-1/38142 "2025-01-16T14:04:23Z")

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Operating system: Windows 10 Slicer version:5.6.2 Hi, I have properly installed Pytorch and other python packages, and restarted and reinstalled Slicer several times. But when I hit Apply, I get this error. I suspect …

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## [The"Markups to Model" is displayed as a radius, not a sphere](https://discourse.slicer.org/t/the-markups-to-model-is-displayed-as-a-radius-not-a-sphere/41115)

<div class="topic-metadata">

**Author:** [@coenwang01](https://discourse.slicer.org/u/coenwang01)\
**Replies:** 2\
**Last updated:** [January 16, 2025, 12:55pm UTC](https://discourse.slicer.org/t/the-markups-to-model-is-displayed-as-a-radius-not-a-sphere/41115 "2025-01-16T12:55:07Z")

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I drew a sphere using the “Shape” function in ExtraMarkups , and then used “Markups to Model” in IGT. However, in the subject hierarchy, the model is only displayed as a radius, not a sphere. Is this a bug?

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## [Different SlicerRT behavior when changing Windows to Linux system](https://discourse.slicer.org/t/different-slicerrt-behavior-when-changing-windows-to-linux-system/41016)

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**Author:** [@Fabio\_Lunelli](https://discourse.slicer.org/u/Fabio_Lunelli)\
**Replies:** 8\
**Last updated:** [January 16, 2025, 12:29pm UTC](https://discourse.slicer.org/t/different-slicerrt-behavior-when-changing-windows-to-linux-system/41016 "2025-01-16T12:29:10Z")

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Hi there, I am using 3D Slicer with the SlicerRT extension to simulate radiotherapy (RT) planning. My workflow involves importing two folders into Slicer: One containing the DICOM images. One containing the contoured …

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## [Recommendations for Computer/Hardware Requirements?](https://discourse.slicer.org/t/recommendations-for-computer-hardware-requirements/41109)

<div class="topic-metadata">

**Author:** [@PhotoJoe](https://discourse.slicer.org/u/PhotoJoe)\
**Replies:** 0\
**Last updated:** [January 16, 2025, 2:40am UTC](https://discourse.slicer.org/t/recommendations-for-computer-hardware-requirements/41109 "2025-01-16T02:40:29Z")

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Hi all, I will be purchasing a new laptop computer for using in a research project related to Ultrasound Transducers and Other cameras connected with Optical trackers and SlicerIGT. I have only a pretty basic knowledge …

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## [Creating and Exporting 2D Bounding Boxes for Each Slice for Deep Learning Training](https://discourse.slicer.org/t/creating-and-exporting-2d-bounding-boxes-for-each-slice-for-deep-learning-training/41102)

<div class="topic-metadata">

**Author:** [@zupl1234](https://discourse.slicer.org/u/zupl1234)\
**Replies:** 1\
**Last updated:** [January 15, 2025, 11:33pm UTC](https://discourse.slicer.org/t/creating-and-exporting-2d-bounding-boxes-for-each-slice-for-deep-learning-training/41102 "2025-01-15T23:33:17Z")

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Hi, I am working on annotating medical images (CT & MRI) using 3D Slicer, and I have the following use case: I need to: Annotate specific regions of interest by creating 2D bounding boxes on each slice individually. E…

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