# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=39

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

**Page:** 40

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## [TorchIO Segmentation](https://discourse.slicer.org/t/torchio-segmentation/43105)

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**Author:** [@j\_bu](https://discourse.slicer.org/u/j_bu)\
**Replies:** 0\
**Last updated:** [May 26, 2025, 3:20pm UTC](https://discourse.slicer.org/t/torchio-segmentation/43105 "2025-05-26T15:20:31Z")

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Hi all, I want to use the extension TorchIO to change my CT Scan. Is there any way to change my segmentation along with it so that the organs are still segmentated? As I tried it the segmentation stayed the same and jus…

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## [Is possible to create segments by color pallete?](https://discourse.slicer.org/t/is-possible-to-create-segments-by-color-pallete/43094)

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**Author:** [@GioM](https://discourse.slicer.org/u/GioM)\
**Replies:** 1\
**Last updated:** [May 25, 2025, 7:44pm UTC](https://discourse.slicer.org/t/is-possible-to-create-segments-by-color-pallete/43094 "2025-05-25T19:44:42Z")

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Hi all, is it possible to select all the voxels of an image by specifying a color? I have some CT maps of the brain that highlight the areas with different colors, the simplest one has only one color per map. This is a…

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## [CT perfusion coregistration to atlas](https://discourse.slicer.org/t/ct-perfusion-coregistration-to-atlas/42561)

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**Author:** [@GioM](https://discourse.slicer.org/u/GioM)\
**Replies:** 2\
**Last updated:** [May 25, 2025, 8:40am UTC](https://discourse.slicer.org/t/ct-perfusion-coregistration-to-atlas/42561 "2025-05-25T08:40:34Z")

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Hi all, starting from the CT perfusion DICOM files I obtained the nifti penumbra VOI. Now I want to check which anatomical areas are affected based on the AAL atlas. I am stuck in the coregistration phase. How can I ad…

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## [Which one is the best method for cbct voxel based registration , voxel based from cmf module sometimes doesnt work even doing same thing again and again](https://discourse.slicer.org/t/which-one-is-the-best-method-for-cbct-voxel-based-registration-voxel-based-from-cmf-module-sometimes-doesnt-work-even-doing-same-thing-again-and-again/43082)

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**Author:** [@Pedro\_Flores](https://discourse.slicer.org/u/Pedro_Flores)\
**Replies:** 0\
**Last updated:** [May 25, 2025, 4:31am UTC](https://discourse.slicer.org/t/which-one-is-the-best-method-for-cbct-voxel-based-registration-voxel-based-from-cmf-module-sometimes-doesnt-work-even-doing-same-thing-again-and-again/43082 "2025-05-25T04:31:53Z")

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I have issues with voxel based from CMf module suddenly it just wont work , wich one is the best method for cbct scaners voxel based comparison ?

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## [Thresholding creates squares](https://discourse.slicer.org/t/thresholding-creates-squares/43076)

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**Author:** [@vivaciousviscera](https://discourse.slicer.org/u/vivaciousviscera)\
**Replies:** 1\
**Last updated:** [May 24, 2025, 2:26pm UTC](https://discourse.slicer.org/t/thresholding-creates-squares/43076 "2025-05-24T14:26:56Z")

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When I press “Apply” after setting the threshold values for my segment, it creates squares instead of smooth painted areas over my structures. Any idea on what’s going on here and how to fix this?

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## [Dental Arch Research](https://discourse.slicer.org/t/dental-arch-research/43060)

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**Author:** [@cekrebs](https://discourse.slicer.org/u/cekrebs)\
**Replies:** 2\
**Last updated:** [May 23, 2025, 9:05pm UTC](https://discourse.slicer.org/t/dental-arch-research/43060 "2025-05-23T21:05:37Z")

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Hi everyone! I am currently trying to compare two scans of lower teeth (one scan of a plastic typodont, one scan of a 3D printed version of the typodont). The STL files of the models after being scanned are almost identi…

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## [Automated Dental Tools ALI fail](https://discourse.slicer.org/t/automated-dental-tools-ali-fail/43059)

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**Author:** [@eric6](https://discourse.slicer.org/u/eric6)\
**Replies:** 1\
**Last updated:** [May 23, 2025, 4:02pm UTC](https://discourse.slicer.org/t/automated-dental-tools-ali-fail/43059 "2025-05-23T16:02:31Z")

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Been trying to run ALI on 5.2.2 but this “ModuleNotFoundError: No module named ‘pydicom.pixels’” keeps popping up. Also tried 5.4.0, 5.6.1, and 5.8.1 and different kinds of error messages appeared. Any fixes to this?

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## [Segmenting CT scans taken by circular acquisition](https://discourse.slicer.org/t/segmenting-ct-scans-taken-by-circular-acquisition/43062)

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**Author:** [@sldamico131](https://discourse.slicer.org/u/sldamico131)\
**Replies:** 1\
**Last updated:** [May 23, 2025, 3:04pm UTC](https://discourse.slicer.org/t/segmenting-ct-scans-taken-by-circular-acquisition/43062 "2025-05-23T15:04:47Z")

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Operating system: mac OS Sequoia Slicer version: 5.8.1 I am trying to segment the ossicles in a seal skull. The CT scans were taken I believe using circular acquisition. When I load them into slicer, there are no slice…

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## [Slicermorph GPA outputData.csv query](https://discourse.slicer.org/t/slicermorph-gpa-outputdata-csv-query/43056)

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**Author:** [@elg67](https://discourse.slicer.org/u/elg67)\
**Replies:** 1\
**Last updated:** [May 23, 2025, 2:59pm UTC](https://discourse.slicer.org/t/slicermorph-gpa-outputdata-csv-query/43056 "2025-05-23T14:59:48Z")

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Hiya! Potentially a silly question but have the landmark data within the outputData.csv file from the GPA Slicermorph module already undergone superimposition? Just wondering if I need to use the gpagen() function before…

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## [how to change the section angle and save it in the files that, when I use other App to open it, the setting is still what I wanted](https://discourse.slicer.org/t/how-to-change-the-section-angle-and-save-it-in-the-files-that-when-i-use-other-app-to-open-it-the-setting-is-still-what-i-wanted/43061)

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**Author:** [@xiaoqian](https://discourse.slicer.org/u/xiaoqian)\
**Replies:** 0\
**Last updated:** [May 23, 2025, 11:10am UTC](https://discourse.slicer.org/t/how-to-change-the-section-angle-and-save-it-in-the-files-that-when-i-use-other-app-to-open-it-the-setting-is-still-what-i-wanted/43061 "2025-05-23T11:10:35Z")

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PC(Mac OS ,3D slicer 5.8.1) My problem is that I do not want to change the actual spatial information or rotate the image itself; instead, I simply want to redefine the default slice orientations so that the data is di…

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## [Morphocloud instance leads to empty black screen](https://discourse.slicer.org/t/morphocloud-instance-leads-to-empty-black-screen/43049)

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**Author:** [@cliftong](https://discourse.slicer.org/u/cliftong)\
**Replies:** 1\
**Last updated:** [May 22, 2025, 11:55pm UTC](https://discourse.slicer.org/t/morphocloud-instance-leads-to-empty-black-screen/43049 "2025-05-22T23:55:18Z")

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I unshelved a new instance (instance-278, g.xl), but it never fully loads, leaving an empty black screen. I can open up the side toolbar, but nothing else. I can’t even right-click to bring up the desktop menu. I tried t…

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## [Turn off Slice edge in 3d view](https://discourse.slicer.org/t/turn-off-slice-edge-in-3d-view/43047)

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**Author:** [@bgoodell](https://discourse.slicer.org/u/bgoodell)\
**Replies:** 1\
**Last updated:** [May 22, 2025, 10:44pm UTC](https://discourse.slicer.org/t/turn-off-slice-edge-in-3d-view/43047 "2025-05-22T22:44:37Z")

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Problem report for Slicer 5.8.1 win-amd64: In settings-\>view I have unchecked the “Show slice edge in 3d” checkbox but after restarting the red, green and yellow rectangular outlines are still shown in the 3d view. it …

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## [Error writing MRML and MRB files on mapped drive](https://discourse.slicer.org/t/error-writing-mrml-and-mrb-files-on-mapped-drive/43029)

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**Author:** [@ezgimercan](https://discourse.slicer.org/u/ezgimercan)\
**Replies:** 1\
**Last updated:** [May 22, 2025, 3:54pm UTC](https://discourse.slicer.org/t/error-writing-mrml-and-mrb-files-on-mapped-drive/43029 "2025-05-22T15:54:08Z")

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I am using latest stable, 5.8.1 on Ubuntu 22.04. I have some research drives mounted with autofs (nfs). Slicer complains that the locations is not writable when I try to save MRB or MRML files. I can save/write/export ev…

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## [How to Hide Specific Toolbars in Custom AppSlicer Build (Markups, Sequence Browser, etc.)](https://discourse.slicer.org/t/how-to-hide-specific-toolbars-in-custom-appslicer-build-markups-sequence-browser-etc/43033)

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**Author:** [@software](https://discourse.slicer.org/u/software)\
**Replies:** 0\
**Last updated:** [May 22, 2025, 8:18am UTC](https://discourse.slicer.org/t/how-to-hide-specific-toolbars-in-custom-appslicer-build-markups-sequence-browser-etc/43033 "2025-05-22T08:18:18Z")

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Hi everyone, I’ve created a custom NewAppSlicer build using Kitware’s 3D Slicer source. Everything is working great, but I’m running into a UI customization issue. From the View \> Toolbars menu, I want to permanently h…

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## [Graphics processor in MorphoCloud not working?](https://discourse.slicer.org/t/graphics-processor-in-morphocloud-not-working/43027)

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**Author:** [@Dave\_Matthews](https://discourse.slicer.org/u/Dave_Matthews)\
**Replies:** 2\
**Last updated:** [May 21, 2025, 8:22pm UTC](https://discourse.slicer.org/t/graphics-processor-in-morphocloud-not-working/43027 "2025-05-21T20:22:15Z")

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I recently initiated a MorphoCloud instance (Instance-277, g3.xl) and it was working great this morning. However, this afternoon I unshelved it and tried to load in the same dataset I was working with earlier. This time…

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## [SlicerUltrasound extension - when might it be updated through the manager?](https://discourse.slicer.org/t/slicerultrasound-extension-when-might-it-be-updated-through-the-manager/43025)

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**Author:** [@Tina\_Kapur](https://discourse.slicer.org/u/Tina_Kapur)\
**Replies:** 1\
**Last updated:** [May 21, 2025, 7:37pm UTC](https://discourse.slicer.org/t/slicerultrasound-extension-when-might-it-be-updated-through-the-manager/43025 "2025-05-21T19:37:54Z")

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Hello, we’ve fixed a few bugs in the SlicerUltrasound extension and would like current users to download it using the extension manager. Where can I look up the status of where it is stuck? Sorry that I don’t know alread…

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## [How to Create and Export En Face Images in 3D Slicer?](https://discourse.slicer.org/t/how-to-create-and-export-en-face-images-in-3d-slicer/43021)

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**Author:** [@Ahmed\_Raza](https://discourse.slicer.org/u/Ahmed_Raza)\
**Replies:** 1\
**Last updated:** [May 21, 2025, 7:01pm UTC](https://discourse.slicer.org/t/how-to-create-and-export-en-face-images-in-3d-slicer/43021 "2025-05-21T19:01:38Z")

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Hi everyone, I’m working with volumetric OCT data in 3D Slicer and would like to generate en face images. Could someone please guide me on: How to create en face views from a 3D volume? How to extract or export these…

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## [Loading and displaying DICOM Structured Reports](https://discourse.slicer.org/t/loading-and-displaying-dicom-structured-reports/42754)

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**Author:** [@DeepaKrishnaswamy](https://discourse.slicer.org/u/DeepaKrishnaswamy)\
**Replies:** 9\
**Last updated:** [May 21, 2025, 6:50pm UTC](https://discourse.slicer.org/t/loading-and-displaying-dicom-structured-reports/42754 "2025-05-21T18:50:19Z")

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Hi, I have been working on some changes to the QuantitativeReporting plugin for loading DICOM Structured Reports. Currently, the extension supports the loading of measurements. Now, we can load and display bounding boxe…

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## [Make it possible to pan in Flood Fill](https://discourse.slicer.org/t/make-it-possible-to-pan-in-flood-fill/43017)

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**Author:** [@Fishguy](https://discourse.slicer.org/u/Fishguy)\
**Replies:** 0\
**Last updated:** [May 21, 2025, 4:58am UTC](https://discourse.slicer.org/t/make-it-possible-to-pan-in-flood-fill/43017 "2025-05-21T04:58:19Z")

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I still use flood fill as a segmentation tool. it seems that the ability to pan by holding down the shift key is not enabled. Clicking on a slice with the shift down elicits the flood fill rather than allowing me to shi…

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## [Please help me to interpret the following running bone texture module](https://discourse.slicer.org/t/please-help-me-to-interpret-the-following-running-bone-texture-module/43008)

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**Author:** [@BsNghia](https://discourse.slicer.org/u/BsNghia)\
**Replies:** 0\
**Last updated:** [May 20, 2025, 6:36am UTC](https://discourse.slicer.org/t/please-help-me-to-interpret-the-following-running-bone-texture-module/43008 "2025-05-20T06:36:47Z")

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Hi, everone, I dont know the parameters unit, so it is so hard to figure out. Thank you!

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## [ZEISS .zinspect microCT conversion](https://discourse.slicer.org/t/zeiss-zinspect-microct-conversion/43000)

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**Author:** [@arumiat](https://discourse.slicer.org/u/arumiat)\
**Replies:** 3\
**Last updated:** [May 20, 2025, 5:46am UTC](https://discourse.slicer.org/t/zeiss-zinspect-microct-conversion/43000 "2025-05-20T05:46:51Z")

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Dear Slicer Community, Does anyone know of any workflows, tools or extensions that would allow the conversion of a ZEISS .zinspect microCT study to be converted to a format readable by Slicer3D or other imaging software…

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## [What Must be my Computer Capacity in Terms of CPU and RAM. Slicer 3D is running Slow.](https://discourse.slicer.org/t/what-must-be-my-computer-capacity-in-terms-of-cpu-and-ram-slicer-3d-is-running-slow/43001)

<div class="topic-metadata">

**Author:** [@khersi](https://discourse.slicer.org/u/khersi)\
**Replies:** 3\
**Last updated:** [May 20, 2025, 5:45am UTC](https://discourse.slicer.org/t/what-must-be-my-computer-capacity-in-terms-of-cpu-and-ram-slicer-3d-is-running-slow/43001 "2025-05-20T05:45:28Z")

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Hello, I have downloaded the latest version of Slicer 3D, in my DELL Laptop. The application is running so slow that I can not create 3D images. Could you please advise how much CPU and RAM I would need to operate 3D Sl…

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## [Input Method Cannot Be Activated in Packaged Slicer on Ubuntu](https://discourse.slicer.org/t/input-method-cannot-be-activated-in-packaged-slicer-on-ubuntu/42958)

<div class="topic-metadata">

**Author:** [@herryliq](https://discourse.slicer.org/u/herryliq)\
**Replies:** 3\
**Last updated:** [May 20, 2025, 5:09am UTC](https://discourse.slicer.org/t/input-method-cannot-be-activated-in-packaged-slicer-on-ubuntu/42958 "2025-05-20T05:09:59Z")

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We encountered an input method issue during custom development based on 3D Slicer 5.6.2. Operating System: Ubuntu 22.04.4 LTS Slicer Version: 5.6.2 (custom build) Problem Description: When running Slicer direc…

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## [How to check line profile of all slice](https://discourse.slicer.org/t/how-to-check-line-profile-of-all-slice/43007)

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**Author:** [@Vikram](https://discourse.slicer.org/u/Vikram)\
**Replies:** 0\
**Last updated:** [May 20, 2025, 4:13am UTC](https://discourse.slicer.org/t/how-to-check-line-profile-of-all-slice/43007 "2025-05-20T04:13:08Z")

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Hello everyone, hope you are all doing well i want to know how to check line profile of all CT scan slices together, not slice by slice.

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## [GPU and CPU rendering on MacBookPro M2 ProMax](https://discourse.slicer.org/t/gpu-and-cpu-rendering-on-macbookpro-m2-promax/29152)

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**Author:** [@Adam\_Summers](https://discourse.slicer.org/u/Adam_Summers)\
**Replies:** 7\
**Last updated:** [May 20, 2025, 12:50am UTC](https://discourse.slicer.org/t/gpu-and-cpu-rendering-on-macbookpro-m2-promax/29152 "2025-05-20T00:50:26Z")

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I have the latest Apple MacBook with Apple silicon, 96GB of RAM running Ventura. I am using the most recent build of Slicer for Mac from 2023-4-25. My fairly large data sets are rendering well, though slowly, using the C…

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## [How can I crop a segmentation to the size of a ROI?](https://discourse.slicer.org/t/how-can-i-crop-a-segmentation-to-the-size-of-a-roi/43003)

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**Author:** [@fabian34](https://discourse.slicer.org/u/fabian34)\
**Replies:** 1\
**Last updated:** [May 19, 2025, 1:45pm UTC](https://discourse.slicer.org/t/how-can-i-crop-a-segmentation-to-the-size-of-a-roi/43003 "2025-05-19T13:45:27Z")

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I have several segmentations I want to 3d-print, that each consist of 15 segments (which are bones in my case). I only want to print a relevant area of the segmentation, due to material and time reasons. Also this area s…

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## [Getting Centerline (vascular modelling toolkit)](https://discourse.slicer.org/t/getting-centerline-vascular-modelling-toolkit/42991)

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**Author:** [@desireeb](https://discourse.slicer.org/u/desireeb)\
**Replies:** 0\
**Last updated:** [May 19, 2025, 1:15am UTC](https://discourse.slicer.org/t/getting-centerline-vascular-modelling-toolkit/42991 "2025-05-19T01:15:06Z")

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Hello: I am trying to extract Centerline (vascular modelling toolkit). After finalising the segmentation, I export visible segments to model. Finally, I click Centerline but the programme shows: failed to compute array …

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## [PyTomography Extension](https://discourse.slicer.org/t/pytomography-extension/41951)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 6\
**Last updated:** [May 18, 2025, 2:28pm UTC](https://discourse.slicer.org/t/pytomography-extension/41951 "2025-05-18T14:28:22Z")

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Dear expert, There is no PyTomography Extension in 3D Slicer version 5.8.1. Please help me add it. Thank you.

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## [Identify HU range for Air on CT image](https://discourse.slicer.org/t/identify-hu-range-for-air-on-ct-image/42950)

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**Author:** [@imbeatriz](https://discourse.slicer.org/u/imbeatriz)\
**Replies:** 10\
**Last updated:** [May 18, 2025, 1:24pm UTC](https://discourse.slicer.org/t/identify-hu-range-for-air-on-ct-image/42950 "2025-05-18T13:24:46Z")

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Hi everyone, I used TotalSegmentator on a CT image, and it successfully segmented all relevant structures. However, I noticed that it does not include a specific label for air that I need. I need to determine the HU ra…

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## [How to set the parameters of N4ITK MRI Bias Correction?](https://discourse.slicer.org/t/how-to-set-the-parameters-of-n4itk-mri-bias-correction/42988)

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**Author:** [@cui](https://discourse.slicer.org/u/cui)\
**Replies:** 0\
**Last updated:** [May 18, 2025, 11:42am UTC](https://discourse.slicer.org/t/how-to-set-the-parameters-of-n4itk-mri-bias-correction/42988 "2025-05-18T11:42:33Z")

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What does BSpine grid resolution represent? Does it represent Pixel Spacing? If the image Pixel Spacing is 138×138×138 mm, should the BSpine grid resolution be set to 138×138×138 when performing N4ITK MRI Bias Correction…

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