# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=163

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

**Page:** 164

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## [Slicermorph - landmark variance](https://discourse.slicer.org/t/slicermorph-landmark-variance/29419)

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**Author:** [@jusopar](https://discourse.slicer.org/u/jusopar)\
**Replies:** 2\
**Last updated:** [May 12, 2023, 12:05am UTC](https://discourse.slicer.org/t/slicermorph-landmark-variance/29419 "2023-05-12T00:05:50Z")

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Hi All, I have a basic question: what do the ellipse colors in landmark variance plot mean? Thank you, Julia

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## [Convert DICOM RT structure set (RS) to NIFTI](https://discourse.slicer.org/t/convert-dicom-rt-structure-set-rs-to-nifti/29354)

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**Author:** [@Luana\_CONTE](https://discourse.slicer.org/u/Luana_CONTE)\
**Replies:** 3\
**Last updated:** [May 11, 2023, 10:44pm UTC](https://discourse.slicer.org/t/convert-dicom-rt-structure-set-rs-to-nifti/29354 "2023-05-11T22:44:45Z")

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Operating system: Windows 11 Pro Slicer version: 5.2.2 Expected behavior: Actual behavior: Hello everybody, I have got some DICOM series with their RS structures and I need to convert them in NIFTI format in a batch…

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## [Rt structure aide](https://discourse.slicer.org/t/rt-structure-aide/29271)

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**Author:** [@Assia\_Benhamla](https://discourse.slicer.org/u/Assia_Benhamla)\
**Replies:** 10\
**Last updated:** [May 11, 2023, 3:08pm UTC](https://discourse.slicer.org/t/rt-structure-aide/29271 "2023-05-11T15:08:02Z")

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Bjr j’ai des contours en format Dicom réalisé sur des images SPECT, maintenant je veux utiliser ces segments sur des images TEP/CT afin de calculer la concentration radioactives de chaque segment, je n’arrive pas à réa…

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## [Best data import practices for microscopy](https://discourse.slicer.org/t/best-data-import-practices-for-microscopy/22056)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 5\
**Last updated:** [May 11, 2023, 1:24pm UTC](https://discourse.slicer.org/t/best-data-import-practices-for-microscopy/22056 "2023-05-11T13:24:20Z")

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We are testing whether we can use Slicer for a project that relies on confocal stacks and I wanted to hear people’s experience. First step is figuring out the data import. The original data comes in Leica’s proprietary …

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## [Slicer 4.1x incompatibility with SlicerJupyter](https://discourse.slicer.org/t/slicer-4-1x-incompatibility-with-slicerjupyter/29408)

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**Author:** [@edwardwang1](https://discourse.slicer.org/u/edwardwang1)\
**Replies:** 2\
**Last updated:** [May 11, 2023, 12:50am UTC](https://discourse.slicer.org/t/slicer-4-1x-incompatibility-with-slicerjupyter/29408 "2023-05-11T00:50:33Z")

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Hi all, I have been using successfully using SlicerJupyter to process imaging data for the last year. Recently, my hard drive was wiped, and I have been unable to replicate my workflow. I have a couple of questions/issu…

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## [Unable to open the saved stl or vtk centerline extraction in other modelling software](https://discourse.slicer.org/t/unable-to-open-the-saved-stl-or-vtk-centerline-extraction-in-other-modelling-software/29372)

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**Author:** [@Yvonne](https://discourse.slicer.org/u/Yvonne)\
**Replies:** 2\
**Last updated:** [May 10, 2023, 10:52pm UTC](https://discourse.slicer.org/t/unable-to-open-the-saved-stl-or-vtk-centerline-extraction-in-other-modelling-software/29372 "2023-05-10T22:52:56Z")

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Hi I’m trying to export the vessel center line and open file in Solidworks and Cura in order to 3D print the structure. However, all of the 3D modelling software showed that the file is corrupted. Can anyone suggest …

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## [Advice on scan acquisition and/or volume processing](https://discourse.slicer.org/t/advice-on-scan-acquisition-and-or-volume-processing/29406)

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**Author:** [@Jonathan\_Millard](https://discourse.slicer.org/u/Jonathan_Millard)\
**Replies:** 2\
**Last updated:** [May 10, 2023, 7:29pm UTC](https://discourse.slicer.org/t/advice-on-scan-acquisition-and-or-volume-processing/29406 "2023-05-10T19:29:08Z")

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I am having issues with generating a smooth segment with sufficient enough resolution to serve my purposes. I have a skull scanned in a medical setting. The Volumes module reports the dimensions are 512x512x44 and the…

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## [Shifted ROIs (exported from LifeX)](https://discourse.slicer.org/t/shifted-rois-exported-from-lifex/29333)

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**Author:** [@leoraffy](https://discourse.slicer.org/u/leoraffy)\
**Replies:** 2\
**Last updated:** [May 10, 2023, 4:12pm UTC](https://discourse.slicer.org/t/shifted-rois-exported-from-lifex/29333 "2023-05-10T16:12:31Z")

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Hi, I am working on a project which requires me to perform radiomics analysis on 3DSlicer on ROIs exported from LifeX. Every ROI exported from LifeX is shifted compared to the PET series when I open it on 3D Slicer, eve…

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## [Nvidia AIAA server](https://discourse.slicer.org/t/nvidia-aiaa-server/29374)

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**Author:** [@marwanabb](https://discourse.slicer.org/u/marwanabb)\
**Replies:** 5\
**Last updated:** [May 10, 2023, 3:01pm UTC](https://discourse.slicer.org/t/nvidia-aiaa-server/29374 "2023-05-10T15:01:48Z")

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Hello, It seems that the remote default server for the Nvidia AIAA module is offline. If I’m not wrong, the server address is : http://perklabseg.cs.queensu.ca:8000/ . Is It normal ?

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## [FOV of live ultrasound image](https://discourse.slicer.org/t/fov-of-live-ultrasound-image/29294)

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**Author:** [@Albags](https://discourse.slicer.org/u/Albags)\
**Replies:** 3\
**Last updated:** [May 10, 2023, 2:28pm UTC](https://discourse.slicer.org/t/fov-of-live-ultrasound-image/29294 "2023-05-10T14:28:46Z")

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Hi, Through the PLUS toolkit I connect an US scanner with 3D slicer. The image I receive includes the US image plus all text and graphics included on the screen of the scanner, however I would like to display only the u…

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## [Determining Modifier labels and what gets a unique identifier](https://discourse.slicer.org/t/determining-modifier-labels-and-what-gets-a-unique-identifier/29192)

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**Author:** [@egrace479](https://discourse.slicer.org/u/egrace479)\
**Replies:** 1\
**Last updated:** [May 10, 2023, 5:01am UTC](https://discourse.slicer.org/t/determining-modifier-labels-and-what-gets-a-unique-identifier/29192 "2023-05-10T05:01:02Z")

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Background: I’m following the segment-context-schema.json (as demonstrated in the slicer docs on GitHub) to programmatically generate new JSON files from CSVs following that schema so we can import them into slicer (spec…

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## [Model Crop is not running](https://discourse.slicer.org/t/model-crop-is-not-running/29343)

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**Author:** [@Muhammed\_Fatih\_Talu](https://discourse.slicer.org/u/Muhammed_Fatih_Talu)\
**Replies:** 1\
**Last updated:** [May 10, 2023, 4:45am UTC](https://discourse.slicer.org/t/model-crop-is-not-running/29343 "2023-05-10T04:45:23Z")

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Because It uses annotationROI which is obsolete and no longer used. It should be updated to MarkupROI. Thanks

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## [Frontal bone thickness within uniform grid](https://discourse.slicer.org/t/frontal-bone-thickness-within-uniform-grid/29239)

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**Author:** [@damiazlkflee](https://discourse.slicer.org/u/damiazlkflee)\
**Replies:** 1\
**Last updated:** [May 10, 2023, 4:42am UTC](https://discourse.slicer.org/t/frontal-bone-thickness-within-uniform-grid/29239 "2023-05-10T04:42:09Z")

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Operating system: Windows 10 Slicer version: 5.2.1 Expected behavior: Calculating thickness within each grid of a uniform grid. Actual behavior: None Hi. I segmented a frontal bone. I want to put a uniform grid with …

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## [TotalSegmentator error at first run: "Command ‘pip’, ‘install’, ‘git+https://github.com/wasserth/TotalSegmentator.git’, ‘–no-deps’\]’ returned non-zero exit status"](https://discourse.slicer.org/t/totalsegmentator-error-at-first-run-command-pip-install-git-https-github-com-wasserth-totalsegmentator-git-no-deps-returned-non-zero-exit-status/26715)

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**Author:** [@miuwells](https://discourse.slicer.org/u/miuwells)\
**Replies:** 43\
**Last updated:** [May 10, 2023, 3:40am UTC](https://discourse.slicer.org/t/totalsegmentator-error-at-first-run-command-pip-install-git-https-github-com-wasserth-totalsegmentator-git-no-deps-returned-non-zero-exit-status/26715 "2023-05-10T03:40:13Z")

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Hi all, I have just tried the extension and it gives me error, I copy the log for help, I have tried to update Pytorch and it also gives me error. I think the extension is amazing the amount of elements that can be segm…

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## [The spline function for spline curve in Markups](https://discourse.slicer.org/t/the-spline-function-for-spline-curve-in-markups/29381)

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**Author:** [@Chuan](https://discourse.slicer.org/u/Chuan)\
**Replies:** 1\
**Last updated:** [May 10, 2023, 2:02am UTC](https://discourse.slicer.org/t/the-spline-function-for-spline-curve-in-markups/29381 "2023-05-10T02:02:55Z")

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Hi, Does anyone how in 3D slicer, which kind of spline curve function is used in markups? I can only see the curve type is spline, but have not found out which kind of function is used for this Spline type. Best re…

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## [SlicerSALT Srep](https://discourse.slicer.org/t/slicersalt-srep/29388)

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**Author:** [@umair04](https://discourse.slicer.org/u/umair04)\
**Replies:** 0\
**Last updated:** [May 10, 2023, 1:56am UTC](https://discourse.slicer.org/t/slicersalt-srep/29388 "2023-05-10T01:56:50Z")

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Operating system: MacOS Slicer version: 5.2.2 Does anyone know if there is a way to quantify the length of the spokes created in a skeletal representation on 3D Slicer?

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## [How to strip skull in 2D CT scans dicom file by python ?](https://discourse.slicer.org/t/how-to-strip-skull-in-2d-ct-scans-dicom-file-by-python/29385)

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**Author:** [@ShangWeiKuo](https://discourse.slicer.org/u/ShangWeiKuo)\
**Replies:** 1\
**Last updated:** [May 10, 2023, 12:55am UTC](https://discourse.slicer.org/t/how-to-strip-skull-in-2d-ct-scans-dicom-file-by-python/29385 "2023-05-10T00:55:50Z")

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Hello. I’ve installed itk-skullstripping by using pip install itk-skullstripping. However. I have no idea the methods to use this package to strip skull in python. My file is 2D CT scans and in the format of dicom. Y…

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## [Cerebrospinal fluid volume and cerebral hemorrhage focus volume were calculated using brain MRI](https://discourse.slicer.org/t/cerebrospinal-fluid-volume-and-cerebral-hemorrhage-focus-volume-were-calculated-using-brain-mri/29355)

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**Author:** [@duan](https://discourse.slicer.org/u/duan)\
**Replies:** 1\
**Last updated:** [May 9, 2023, 1:54pm UTC](https://discourse.slicer.org/t/cerebrospinal-fluid-volume-and-cerebral-hemorrhage-focus-volume-were-calculated-using-brain-mri/29355 "2023-05-09T13:54:45Z")

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I am very grateful for your recent reply, which solved many problems for me, and I would like to thank you from the bottom of my heart. I have some questions about MRI again, and I would like to ask you about it. I would…

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## [3D Slicer and MONAI receive recognition at the GTA Digital September 2022](https://discourse.slicer.org/t/3d-slicer-and-monai-receive-recognition-at-the-gta-digital-september-2022/29376)

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**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 0\
**Last updated:** [May 9, 2023, 9:49am UTC](https://discourse.slicer.org/t/3d-slicer-and-monai-receive-recognition-at-the-gta-digital-september-2022/29376 "2023-05-09T09:49:36Z")

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It is noteworthy that MONAI and 3D Slicer have been mentioned in an extended passage within the session titled “The Rise of Transformer AI and Digital Twins in Healthcare” by Kimberly Powell, General Manager and VP, Heal…

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## [SlicerMorph / GPA - select samples that form the mean shape?](https://discourse.slicer.org/t/slicermorph-gpa-select-samples-that-form-the-mean-shape/29369)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 0\
**Last updated:** [May 9, 2023, 8:15am UTC](https://discourse.slicer.org/t/slicermorph-gpa-select-samples-that-form-the-mean-shape/29369 "2023-05-09T08:15:20Z")

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Hi, currently I am analysing several skulls; the plan is to use a subgroup of these skulls for generating the “mean shape” and then to compute the GP-distance of all skulls based on this selected “mean shape”. Is the…

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## [.seg.nrrd and .nrrd to dicom](https://discourse.slicer.org/t/seg-nrrd-and-nrrd-to-dicom/29306)

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**Author:** [@Jason\_Zheng](https://discourse.slicer.org/u/Jason_Zheng)\
**Replies:** 3\
**Last updated:** [May 8, 2023, 11:37pm UTC](https://discourse.slicer.org/t/seg-nrrd-and-nrrd-to-dicom/29306 "2023-05-08T23:37:12Z")

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Operating system:Windows 11 Slicer version:3D slicer 5.2.2 Expected behavior:I want to export the seg.nrrd file together with the original nrrd file as a dicom file Actual behavior:Now package and export together, and…

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## [How to export the overlap MR images in the slice view](https://discourse.slicer.org/t/how-to-export-the-overlap-mr-images-in-the-slice-view/29340)

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**Author:** [@Eugene\_Zh](https://discourse.slicer.org/u/Eugene_Zh)\
**Replies:** 1\
**Last updated:** [May 8, 2023, 2:51pm UTC](https://discourse.slicer.org/t/how-to-export-the-overlap-mr-images-in-the-slice-view/29340 "2023-05-08T14:51:47Z")

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Operating system: Windows 11 Slicer version: 5.2.2 Dear All, I have two different MR Sequences that is already registered, but not the same FOV. I can overlap them in the slice view by using the foreground-background …

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## [3D slicer only showing one slice](https://discourse.slicer.org/t/3d-slicer-only-showing-one-slice/29339)

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**Author:** [@Chloe\_Lai](https://discourse.slicer.org/u/Chloe_Lai)\
**Replies:** 1\
**Last updated:** [May 8, 2023, 2:44pm UTC](https://discourse.slicer.org/t/3d-slicer-only-showing-one-slice/29339 "2023-05-08T14:44:26Z")

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I imported all slices and segmented successfully, but the next time i opened the mrml file to continue segmenting, it only shows one slice/image. How do i fix this without having to start over and upload the data again?

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## [Is there any difference between nrrd converted by plastimatch and slicer? What algorithm is used by slicer to convert to nrrd](https://discourse.slicer.org/t/is-there-any-difference-between-nrrd-converted-by-plastimatch-and-slicer-what-algorithm-is-used-by-slicer-to-convert-to-nrrd/29026)

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**Author:** [@b\_s\_umesh\_sherkhane](https://discourse.slicer.org/u/b_s_umesh_sherkhane)\
**Replies:** 6\
**Last updated:** [May 8, 2023, 2:26pm UTC](https://discourse.slicer.org/t/is-there-any-difference-between-nrrd-converted-by-plastimatch-and-slicer-what-algorithm-is-used-by-slicer-to-convert-to-nrrd/29026 "2023-05-08T14:26:14Z")

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Hi , I am trying to extract radiomics from PET dicom. I converted the dicom to nrrd using two methods. using slicer i saved the image and mask to nrrd Using plastimatch i converted the dicom to nrrd. When i run pyrad…

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## [Exporting Centerline Data to Fusion 360](https://discourse.slicer.org/t/exporting-centerline-data-to-fusion-360/24546)

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**Author:** [@Busayo101](https://discourse.slicer.org/u/Busayo101)\
**Replies:** 1\
**Last updated:** [May 8, 2023, 2:22pm UTC](https://discourse.slicer.org/t/exporting-centerline-data-to-fusion-360/24546 "2023-05-08T14:22:32Z")

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Hello! I am trying to take a Centerline and bring it into Fusion 360 in the same orientation. Is it possible to convert it into a spline or some sort to be able to refrence it in Fusion 360? No matter what format I do…

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## [Add segmentation with sphere brush from known coordinates via scripts](https://discourse.slicer.org/t/add-segmentation-with-sphere-brush-from-known-coordinates-via-scripts/29321)

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**Author:** [@hapkx](https://discourse.slicer.org/u/hapkx)\
**Replies:** 4\
**Last updated:** [May 8, 2023, 12:55pm UTC](https://discourse.slicer.org/t/add-segmentation-with-sphere-brush-from-known-coordinates-via-scripts/29321 "2023-05-08T12:55:34Z")

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This problem may be simple, but I can’t find the right solution for the moment. There are some coordinates, for example(10, 10, 10) and (20, 20, 20), and I want to add ‘paint’ (maybe with a sphere brush) at the correspo…

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## [How do I create gridlines in 3D view](https://discourse.slicer.org/t/how-do-i-create-gridlines-in-3d-view/29301)

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**Author:** [@q2577040659](https://discourse.slicer.org/u/q2577040659)\
**Replies:** 2\
**Last updated:** [May 8, 2023, 1:31am UTC](https://discourse.slicer.org/t/how-do-i-create-gridlines-in-3d-view/29301 "2023-05-08T01:31:25Z")

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How to create gridlines in 3D view, similar to the effect in the figure.

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## [Error message running covariate significiance testing module](https://discourse.slicer.org/t/error-message-running-covariate-significiance-testing-module/27921)

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**Author:** [@r0320](https://discourse.slicer.org/u/r0320)\
**Replies:** 1\
**Last updated:** [May 7, 2023, 8:14pm UTC](https://discourse.slicer.org/t/error-message-running-covariate-significiance-testing-module/27921 "2023-05-07T20:14:26Z")

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After running the covariate significiance testing module on slicer 4.0.1, I obtain the differents outocomes but I also have this error message : MFSDA\_run standard error: C:\\Program Files\\SlicerSALT 4.0.1\\lib\\SlicerSAL…

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## [Slicer-Python Packages Use and Install](https://discourse.slicer.org/t/slicer-python-packages-use-and-install/984)

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**Author:** [@ssyip](https://discourse.slicer.org/u/ssyip)\
**Replies:** 67\
**Last updated:** [March 31, 2023, 3:17pm UTC](https://discourse.slicer.org/t/slicer-python-packages-use-and-install/984 "2023-03-31T15:17:34Z")

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Hi, There are python packages (e.g. scipy) that I would like to use but not installed under "Slicer 4.6.2\\lib\\Python\\Lib\\site-packages". If I already have Python 2.7 and all packages I want installed on my computer,…

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## [How to disable synchronous marking of axial and sagittal slice](https://discourse.slicer.org/t/how-to-disable-synchronous-marking-of-axial-and-sagittal-slice/29253)

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**Author:** [@PolinaPostnikova](https://discourse.slicer.org/u/PolinaPostnikova)\
**Replies:** 3\
**Last updated:** [May 6, 2023, 6:11pm UTC](https://discourse.slicer.org/t/how-to-disable-synchronous-marking-of-axial-and-sagittal-slice/29253 "2023-05-06T18:11:36Z")

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Hello. Could you please tell me how to disable synchronous marking of axial and sagittal slice on MRI? Thanx

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