# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=213

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

**Page:** 214

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## [GPA 3D model and Landmarks not lining up](https://discourse.slicer.org/t/gpa-3d-model-and-landmarks-not-lining-up/24520)

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**Author:** [@ejames26](https://discourse.slicer.org/u/ejames26)\
**Replies:** 0\
**Last updated:** [July 27, 2022, 7:08am UTC](https://discourse.slicer.org/t/gpa-3d-model-and-landmarks-not-lining-up/24520 "2022-07-27T07:08:04Z")

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Hello Everyone, I am having some trouble getting my segmentation model to align with landmarks in my GPA analysis. Landmarks were placed on volume renders from tiff stack images with spacing representative of the resol…

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## [radiomics module for ultrasound](https://discourse.slicer.org/t/radiomics-module-for-ultrasound/24516)

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**Author:** [@rrad](https://discourse.slicer.org/u/rrad)\
**Replies:** 0\
**Last updated:** [July 27, 2022, 6:14am UTC](https://discourse.slicer.org/t/radiomics-module-for-ultrasound/24516 "2022-07-27T06:14:14Z")

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Operating system:mac0s Slicer version: 5.0.3 Expected behavior: Actual behavior: I am having difficulty in obtaining radiomic values from regions of interest drawn on .dcm ultrasound images. In particular, when I sele…

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## [Multiply two images using "Multiply Scalar Volumes" or "Mask Scalar Volume" and save the resulting image (using Python)](https://discourse.slicer.org/t/multiply-two-images-using-multiply-scalar-volumes-or-mask-scalar-volume-and-save-the-resulting-image-using-python/10947)

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**Author:** [@Vishal\_P](https://discourse.slicer.org/u/Vishal_P)\
**Replies:** 8\
**Last updated:** [July 26, 2022, 8:14pm UTC](https://discourse.slicer.org/t/multiply-two-images-using-multiply-scalar-volumes-or-mask-scalar-volume-and-save-the-resulting-image-using-python/10947 "2022-07-26T20:14:20Z")

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I am a beginner trying to automate some tasks in 3D Slicer using Python. I have a mask image and another input volume image both in nifti format. how can I use python to automate the multiplication between two images a…

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## [Export mean HU values along path (or tube)](https://discourse.slicer.org/t/export-mean-hu-values-along-path-or-tube/24503)

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**Author:** [@Pepper](https://discourse.slicer.org/u/Pepper)\
**Replies:** 1\
**Last updated:** [July 26, 2022, 5:23pm UTC](https://discourse.slicer.org/t/export-mean-hu-values-along-path-or-tube/24503 "2022-07-26T17:23:13Z")

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Hello all, I have a spiral structure, difficult to segment because of its shape and the gradient of density in it. I would like to analyse this increasing gradient of density, and export the HU values all along the spi…

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## [Tracked-Ultrasound with external image data adjustments \[Matlab\]](https://discourse.slicer.org/t/tracked-ultrasound-with-external-image-data-adjustments-matlab/24499)

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**Author:** [@J.vd.Zee](https://discourse.slicer.org/u/J.vd.Zee)\
**Replies:** 0\
**Last updated:** [July 26, 2022, 2:19pm UTC](https://discourse.slicer.org/t/tracked-ultrasound-with-external-image-data-adjustments-matlab/24499 "2022-07-26T14:19:07Z")

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I have a Tracked-Ultrasound system that combines tracking information and image data. Within this set-up I would like to export the imaging data to Matlab, make adjustments (segmentation), and import again. As the image…

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## [Create GridTransform from 3d motion field](https://discourse.slicer.org/t/create-gridtransform-from-3d-motion-field/24496)

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**Author:** [@llafitte007](https://discourse.slicer.org/u/llafitte007)\
**Replies:** 1\
**Last updated:** [July 26, 2022, 1:11pm UTC](https://discourse.slicer.org/t/create-gridtransform-from-3d-motion-field/24496 "2022-07-26T13:11:14Z")

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Hi, I am developing a motion estimation module based on an existing library ; the result of the estimate is 3d vector field of type numpy array (shape = (width, height, depth, 3)) plus other fields (origin, spacing, …). …

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## [Unable to open 3D Slicer](https://discourse.slicer.org/t/unable-to-open-3d-slicer/24489)

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**Author:** [@HannahD](https://discourse.slicer.org/u/HannahD)\
**Replies:** 1\
**Last updated:** [July 26, 2022, 1:12am UTC](https://discourse.slicer.org/t/unable-to-open-3d-slicer/24489 "2022-07-26T01:12:56Z")

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Hello, I am running Windows 10, and I’m having issues opening the 3D Slicer app. A couple months ago, I had downloaded version 5.0.2, and after installing it, I was able to open and use the program without any issues. I…

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## [Connect segmentation sequence to volume sequence.](https://discourse.slicer.org/t/connect-segmentation-sequence-to-volume-sequence/24490)

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**Author:** [@pitfall24](https://discourse.slicer.org/u/pitfall24)\
**Replies:** 0\
**Last updated:** [July 25, 2022, 8:12pm UTC](https://discourse.slicer.org/t/connect-segmentation-sequence-to-volume-sequence/24490 "2022-07-25T20:12:02Z")

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This is a bit of a continuation of this topic. I have a set of volumes which are “4D” meaning they are 3D nifti files which span over a period of time. I also have pre-made corresponding segmentations in the same format.…

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## [Draw a line connecting 2 landmarks using Python](https://discourse.slicer.org/t/draw-a-line-connecting-2-landmarks-using-python/24291)

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**Author:** [@l2022](https://discourse.slicer.org/u/l2022)\
**Replies:** 2\
**Last updated:** [July 25, 2022, 12:43pm UTC](https://discourse.slicer.org/t/draw-a-line-connecting-2-landmarks-using-python/24291 "2022-07-25T12:43:50Z")

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Hi, Could you please tell me how I can add a line in the 3D view connecting 2 specific landmarks using Python in Slicer? Thank you

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## [Fail to export PET dicom files](https://discourse.slicer.org/t/fail-to-export-pet-dicom-files/22410)

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**Author:** [@collamaf](https://discourse.slicer.org/u/collamaf)\
**Replies:** 3\
**Last updated:** [July 25, 2022, 9:22am UTC](https://discourse.slicer.org/t/fail-to-export-pet-dicom-files/22410 "2022-07-25T09:22:30Z")

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Operating system: MacOs 12.2.1 Slicer version: 4.13.0-2021-12-28 Expected behavior: Being able to export a just imported PET Dicom series Actual behavior: “Creating DICOM files from scalar volume failed” Hello everbo…

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## [coverted model to segmentations over-smoothing](https://discourse.slicer.org/t/coverted-model-to-segmentations-over-smoothing/24475)

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**Author:** [@Tao](https://discourse.slicer.org/u/Tao)\
**Replies:** 0\
**Last updated:** [July 25, 2022, 9:18am UTC](https://discourse.slicer.org/t/coverted-model-to-segmentations-over-smoothing/24475 "2022-07-25T09:18:03Z")

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Hi, I loaded the vtp file as a 3d render, but I want to use scissors, I converted the model to segmentations, there is over-smoothing, how to avoid the change,or how to use the scissors tool directly on the model T…

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## [How better make teeth segmentation? ](https://discourse.slicer.org/t/how-better-make-teeth-segmentation/24467)

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**Author:** [@radiodid](https://discourse.slicer.org/u/radiodid)\
**Replies:** 1\
**Last updated:** [July 25, 2022, 8:21am UTC](https://discourse.slicer.org/t/how-better-make-teeth-segmentation/24467 "2022-07-25T08:21:02Z")

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I need to make segmentation and 3D reconstruction of only the teeth, without the jaw. Does anyone use or know of any methods that could help me with this task? What additional plugins can be used to improve performance?

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## [Extract 3D Coordinates from VTK Output File](https://discourse.slicer.org/t/extract-3d-coordinates-from-vtk-output-file/15391)

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**Author:** [@Judith](https://discourse.slicer.org/u/Judith)\
**Replies:** 6\
**Last updated:** [July 24, 2022, 10:32pm UTC](https://discourse.slicer.org/t/extract-3d-coordinates-from-vtk-output-file/15391 "2022-07-24T22:32:45Z")

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Hello everybody, How do you extract de 3D coordinates from a VTK output file? This VTK output file is created using the Model-to-Model Distance module. It does not matter if the coordinates are in the LPS or RAS system,…

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## [Issue loading VTK file](https://discourse.slicer.org/t/issue-loading-vtk-file/24469)

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**Author:** [@jsalas424](https://discourse.slicer.org/u/jsalas424)\
**Replies:** 3\
**Last updated:** [July 24, 2022, 9:46pm UTC](https://discourse.slicer.org/t/issue-loading-vtk-file/24469 "2022-07-24T21:46:48Z")

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Hello, I generated a VTK file matlab using vtkwrite from triangle mesh data. The raw data looks like this: 16.2150000000000 13.2360000000000 126.065000000000 16.1490000000000 14.2370000000000 125.708000000000 16.8430…

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## [slicer cannot find path separator](https://discourse.slicer.org/t/slicer-cannot-find-path-separator/24466)

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**Author:** [@Xin\_Chen](https://discourse.slicer.org/u/Xin_Chen)\
**Replies:** 1\
**Last updated:** [July 24, 2022, 3:56pm UTC](https://discourse.slicer.org/t/slicer-cannot-find-path-separator/24466 "2022-07-24T15:56:42Z")

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Hello everyone I used Slicer 5.1.0 (Preview Release) on Win 10 (64 bit). Now, I want to open the extension Module from github. I succefully add the path of Module in Edit tab. However, when I execute the module, Slicer…

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## [Slicer 4.10.2 Model Imports](https://discourse.slicer.org/t/slicer-4-10-2-model-imports/24460)

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**Author:** [@ChristophG123](https://discourse.slicer.org/u/ChristophG123)\
**Replies:** 2\
**Last updated:** [July 23, 2022, 5:22am UTC](https://discourse.slicer.org/t/slicer-4-10-2-model-imports/24460 "2022-07-23T05:22:12Z")

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I’m trying to import stl files from my PC on Slicer 4.10.2 because I’m modifying an old module that doesn’t work on newer versions of Slicer. However, it seems like the code I normally use on Slicer 5.1.0 doesn’t work fo…

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## [Best tools to analyze spongy bone/ trabecular bone ?](https://discourse.slicer.org/t/best-tools-to-analyze-spongy-bone-trabecular-bone/24457)

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**Author:** [@Marjan\_Khan](https://discourse.slicer.org/u/Marjan_Khan)\
**Replies:** 1\
**Last updated:** [July 22, 2022, 10:52pm UTC](https://discourse.slicer.org/t/best-tools-to-analyze-spongy-bone-trabecular-bone/24457 "2022-07-22T22:52:31Z")

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Hi, I use the Bone thickness tool to analyze Cortical Bone, but curious as to what extensions/ plug-ins I can use to analyze porosity/ deterioration of trabecular bone. Any feedback would be greatly appreciated! Thanks! …

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## [T2\* mapping using T2 mapping extensions](https://discourse.slicer.org/t/t2-mapping-using-t2-mapping-extensions/24455)

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**Author:** [@SHAK](https://discourse.slicer.org/u/SHAK)\
**Replies:** 0\
**Last updated:** [July 22, 2022, 6:08pm UTC](https://discourse.slicer.org/t/t2-mapping-using-t2-mapping-extensions/24455 "2022-07-22T18:08:13Z")

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Can we measure T2\* using T2 mapping extensions? For example using GitHub - gattia/Slicer-T2mapping Or are there any specific extensions available for T2\* mapping?

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## [Where has local thresholding gone 5.03?](https://discourse.slicer.org/t/where-has-local-thresholding-gone-5-03/24451)

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**Author:** [@sandigeeup](https://discourse.slicer.org/u/sandigeeup)\
**Replies:** 4\
**Last updated:** [July 22, 2022, 3:42pm UTC](https://discourse.slicer.org/t/where-has-local-thresholding-gone-5-03/24451 "2022-07-22T15:42:23Z")

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Hi, I no longer have local threshold in the 5.03 version of slicer? I have a few options missing, can you advise please. Thank you :slight\_smile:

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## [Question on pedicle screw planner and simulator output](https://discourse.slicer.org/t/question-on-pedicle-screw-planner-and-simulator-output/24450)

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**Author:** [@Yao\_Li](https://discourse.slicer.org/u/Yao_Li)\
**Replies:** 0\
**Last updated:** [July 22, 2022, 1:20pm UTC](https://discourse.slicer.org/t/question-on-pedicle-screw-planner-and-simulator-output/24450 "2022-07-22T13:20:36Z")

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I want to output the segmented spine with the pedicle screws in separated .obj files. But I don’t know how to do it with pedicle screw planner or simulator extensions. Any one has any idea?

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## [Convert .mhd file to a 3D image that can be saved as a .ply](https://discourse.slicer.org/t/convert-mhd-file-to-a-3d-image-that-can-be-saved-as-a-ply/24440)

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**Author:** [@aotero54](https://discourse.slicer.org/u/aotero54)\
**Replies:** 1\
**Last updated:** [July 21, 2022, 9:48pm UTC](https://discourse.slicer.org/t/convert-mhd-file-to-a-3d-image-that-can-be-saved-as-a-ply/24440 "2022-07-21T21:48:02Z")

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Hello, I have several mhd files that I am trying to convert into a 3D image that can be saved as a ply and thus have landmarks placed upon it. I am unsure of how to do this and other similar posts I have found have not …

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## [How could I get the real-time rotation angles of the 3D image? SOS!](https://discourse.slicer.org/t/how-could-i-get-the-real-time-rotation-angles-of-the-3d-image-sos/21997)

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**Author:** [@gavinricky](https://discourse.slicer.org/u/gavinricky)\
**Replies:** 1\
**Last updated:** [July 21, 2022, 7:06pm UTC](https://discourse.slicer.org/t/how-could-i-get-the-real-time-rotation-angles-of-the-3d-image-sos/21997 "2022-07-21T19:06:06Z")

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Operating system:windows Slicer version:4.8.1 Hi everyone, I want to know how to get the real-time rotation angles of the 3D image? Thus, I can know the degree of rotation of the C-arm during surgery. I’ve seen pe…

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## [3D Slicer customized application with display and GPU on different hosts](https://discourse.slicer.org/t/3d-slicer-customized-application-with-display-and-gpu-on-different-hosts/24434)

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**Author:** [@Lee\_Newberg](https://discourse.slicer.org/u/Lee_Newberg)\
**Replies:** 3\
**Last updated:** [July 21, 2022, 5:55pm UTC](https://discourse.slicer.org/t/3d-slicer-customized-application-with-display-and-gpu-on-different-hosts/24434 "2022-07-21T17:55:54Z")

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Others have written a very nice lung-air app customization of 3D Slicer that makes use of a GPU. I have a display-less Ubuntu 20.04 workstation with a good GPU and an Ubuntu 20.04 laptop with a display but a poor GPU. …

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## [Anatomical brain segmentation](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778)

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**Author:** [@Miglius\_Mikalauskas](https://discourse.slicer.org/u/Miglius_Mikalauskas)\
**Replies:** 5\
**Last updated:** [July 21, 2022, 3:49pm UTC](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778 "2022-07-21T15:49:27Z")

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Hi. Is there a way to automatically segment human brain in mri by anatomical structures? So that i could automatically see the human brain segmented by either lobes (frontal, temporal etc) or by gyri? The photo is f…

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## [How can I find the error log after a crash?](https://discourse.slicer.org/t/how-can-i-find-the-error-log-after-a-crash/24389)

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**Author:** [@wrc](https://discourse.slicer.org/u/wrc)\
**Replies:** 4\
**Last updated:** [July 21, 2022, 9:27am UTC](https://discourse.slicer.org/t/how-can-i-find-the-error-log-after-a-crash/24389 "2022-07-21T09:27:38Z")

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Hi, I am developing an extension based on ParrallelProcessing. It works well in most cases but fails sometimes. The 3D Slicer window closes automatically during calculation. So I cannot find the log on view-error log. Do…

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## [2D nifti sagittal slice won't open in 3DSlicer](https://discourse.slicer.org/t/2d-nifti-sagittal-slice-wont-open-in-3dslicer/24407)

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**Author:** [@BayesMonk](https://discourse.slicer.org/u/BayesMonk)\
**Replies:** 8\
**Last updated:** [July 21, 2022, 8:16am UTC](https://discourse.slicer.org/t/2d-nifti-sagittal-slice-wont-open-in-3dslicer/24407 "2022-07-21T08:16:37Z")

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Hi, I have a 2D sagittal slice stored in Nifti. It won’t open in slicer and I get the following error: Exception thrown in event: D:\\D\\S\\Slicer-1-build\\ITK\\Modules\\Core\\Common\\include\\itkImageBase.hxx:184: itk::ERROR…

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## [New feature: Automatic update of extensions](https://discourse.slicer.org/t/new-feature-automatic-update-of-extensions/24416)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 0\
**Last updated:** [July 20, 2022, 5:52pm UTC](https://discourse.slicer.org/t/new-feature-automatic-update-of-extensions/24416 "2022-07-20T17:52:40Z")

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We have implemented some long-awaited improvements in the Extensions Manager in Slicer-5.0.3. Most importantly extensions can be updated automatically and bookmarks can be used for convenient reinstallation of a list of …

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## [About displaying MNI atlas on patient head MRI](https://discourse.slicer.org/t/about-displaying-mni-atlas-on-patient-head-mri/23759)

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**Author:** [@Lin](https://discourse.slicer.org/u/Lin)\
**Replies:** 8\
**Last updated:** [July 1, 2022, 7:57am UTC](https://discourse.slicer.org/t/about-displaying-mni-atlas-on-patient-head-mri/23759 "2022-07-01T07:57:15Z")

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Hi I’m new to use slicer. Can someone point me a bit on how to display the atlases (eg. MNI 2009 atlas or others used by Lead DBS) on patient space MRI images? I tried by dragging the atlas onto slicer, but the center is…

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## [Slicer rhomboid voxels in 3D-View](https://discourse.slicer.org/t/slicer-rhomboid-voxels-in-3d-view/24361)

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**Author:** [@chris\_nik](https://discourse.slicer.org/u/chris_nik)\
**Replies:** 9\
**Last updated:** [July 20, 2022, 12:29pm UTC](https://discourse.slicer.org/t/slicer-rhomboid-voxels-in-3d-view/24361 "2022-07-20T12:29:03Z")

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Hello, First of all, thank you again for creating Slicer, it really helps my research a lot. I have the following problem/ question. I am trying to import a 3D-Skeleton.tif (created in ImageJ, width of the skeleton str…

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## [ModuleWizard script problems](https://discourse.slicer.org/t/modulewizard-script-problems/24401)

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**Author:** [@torquil](https://discourse.slicer.org/u/torquil)\
**Replies:** 0\
**Last updated:** [July 20, 2022, 5:33am UTC](https://discourse.slicer.org/t/modulewizard-script-problems/24401 "2022-07-20T05:33:21Z")

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Hi! I’m going to create a new module. I followed a tutorial which told med to download the source code and run the following: python3 ./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/ScriptedLoadableE…

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