# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=207

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

**Page:** 208

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## [How does the Landmark registration get the "from" position](https://discourse.slicer.org/t/how-does-the-landmark-registration-get-the-from-position/25036)

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**Author:** [@whu](https://discourse.slicer.org/u/whu)\
**Replies:** 0\
**Last updated:** [September 1, 2022, 3:39am UTC](https://discourse.slicer.org/t/how-does-the-landmark-registration-get-the-from-position/25036 "2022-09-01T03:39:22Z")

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Hi, In order to make a realtime EM tracker on the physical model, and the needle followed in the virtual model, I tried the Landmark registration tutorial in IGT. Firstly, using the vtkLandmarkTransform, I can get the …

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## [Utilizing Slicer to Calculate 3D Length/ Distance as well as Surface Area on CT Images](https://discourse.slicer.org/t/utilizing-slicer-to-calculate-3d-length-distance-as-well-as-surface-area-on-ct-images/25035)

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**Author:** [@trent.schimmel](https://discourse.slicer.org/u/trent.schimmel)\
**Replies:** 2\
**Last updated:** [September 1, 2022, 2:13am UTC](https://discourse.slicer.org/t/utilizing-slicer-to-calculate-3d-length-distance-as-well-as-surface-area-on-ct-images/25035 "2022-09-01T02:13:22Z")

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Hello All, I’m new to the Slicer community and having a little difficulty getting started on a project. I am looking to calculate 3D length measurements as well as surface area measurements for a set of cranial CT scan…

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## [NaN or infinite value in the segment(.nrrd)](https://discourse.slicer.org/t/nan-or-infinite-value-in-the-segment-nrrd/25027)

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**Author:** [@hourglassnam](https://discourse.slicer.org/u/hourglassnam)\
**Replies:** 0\
**Last updated:** [August 31, 2022, 2:21pm UTC](https://discourse.slicer.org/t/nan-or-infinite-value-in-the-segment-nrrd/25027 "2022-08-31T14:21:59Z")

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Hello, I have been trying to train monailabel from scratch with 10 segmentations I created. I changed the label\_values in following 3 files and changed pretrained to false. Anaconda3\\Lib\\site-packages\\monai\\apps\\deep…

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## [How to change the curvature of the markups plane](https://discourse.slicer.org/t/how-to-change-the-curvature-of-the-markups-plane/24995)

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**Author:** [@1023185654](https://discourse.slicer.org/u/1023185654)\
**Replies:** 8\
**Last updated:** [August 31, 2022, 3:10am UTC](https://discourse.slicer.org/t/how-to-change-the-curvature-of-the-markups-plane/24995 "2022-08-31T03:10:29Z")

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Hello, everyone. Recently, i used markups plane, Then I found out that Plan has rotation and translate functions, but i want that plane also can change the curvature and retaining the translation and rotation functions.

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## [Taking X-Ray Data into CAD Software to run analysis](https://discourse.slicer.org/t/taking-x-ray-data-into-cad-software-to-run-analysis/25011)

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**Author:** [@seths](https://discourse.slicer.org/u/seths)\
**Replies:** 3\
**Last updated:** [August 31, 2022, 3:00am UTC](https://discourse.slicer.org/t/taking-x-ray-data-into-cad-software-to-run-analysis/25011 "2022-08-31T03:00:40Z")

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Hello - I am a mechanical engineer and a brand new user of Slicer3D. I have some X-ray data of a spine and I am wanting to bring parts of that data into a Finite Element Analysis software to apply different loading condi…

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## [How do I properly connect the qMRMLSegmentEditorWidget so that it properly updates?](https://discourse.slicer.org/t/how-do-i-properly-connect-the-qmrmlsegmenteditorwidget-so-that-it-properly-updates/24940)

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**Author:** [@Kevin.Kn](https://discourse.slicer.org/u/Kevin.Kn)\
**Replies:** 4\
**Last updated:** [August 31, 2022, 2:53am UTC](https://discourse.slicer.org/t/how-do-i-properly-connect-the-qmrmlsegmenteditorwidget-so-that-it-properly-updates/24940 "2022-08-31T02:53:12Z")

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I am expanding an automated segmentation Tool that I have created to be a bit more user friendly for people to not go between a ton of menus in slicer. I have a UI created that has the qMRMLSegmentEditorWidget added, an…

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## [Does 3D Slicer segment in 2D or 3D?](https://discourse.slicer.org/t/does-3d-slicer-segment-in-2d-or-3d/25012)

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**Author:** [@O123456789](https://discourse.slicer.org/u/O123456789)\
**Replies:** 1\
**Last updated:** [August 30, 2022, 5:59pm UTC](https://discourse.slicer.org/t/does-3d-slicer-segment-in-2d-or-3d/25012 "2022-08-30T17:59:19Z")

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Hello, I was asked if 3D slicer works in 2D or in 3D, but i wasn’t sure how to answer that. Does the semiautomatic segmentation work on a single slice and then move to the next one or does it spread in all three dimens…

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## [Scribbles update gives "Failed to post process label on MONAI Label Server using Histogram+GraphCut" error](https://discourse.slicer.org/t/scribbles-update-gives-failed-to-post-process-label-on-monai-label-server-using-histogram-graphcut-error/25010)

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**Author:** [@lukasvanderstricht](https://discourse.slicer.org/u/lukasvanderstricht)\
**Replies:** 0\
**Last updated:** [August 30, 2022, 5:51pm UTC](https://discourse.slicer.org/t/scribbles-update-gives-failed-to-post-process-label-on-monai-label-server-using-histogram-graphcut-error/25010 "2022-08-30T17:51:05Z")

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Hi, I am working in Windows and I was able to install MONAILabel and run the exemplary server with the radiology app and the Task09\_Spleen dataset. I am able to see the images in 3D Slicer and everything seems normal. …

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## [MALPACA only runs on the first target model. ](https://discourse.slicer.org/t/malpaca-only-runs-on-the-first-target-model/25009)

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**Author:** [@violetsky](https://discourse.slicer.org/u/violetsky)\
**Replies:** 0\
**Last updated:** [August 30, 2022, 5:50pm UTC](https://discourse.slicer.org/t/malpaca-only-runs-on-the-first-target-model/25009 "2022-08-30T17:50:53Z")

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Hi. I am trying to run MALPACA using 7 templates that I chose (not using the “template selection”). I tried to run the module on a folder containing 60 models. When I run MALPACA it only runs on the first model and stops…

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## [Running external python file from](https://discourse.slicer.org/t/running-external-python-file-from/25002)

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**Author:** [@AMK](https://discourse.slicer.org/u/AMK)\
**Replies:** 1\
**Last updated:** [August 30, 2022, 3:57pm UTC](https://discourse.slicer.org/t/running-external-python-file-from/25002 "2022-08-30T15:57:41Z")

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Hi, I have developed a deep learning model for segmentation. For the purpose of inference, I want to run a python file from Slicer. What commands should I use for this purpose?

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## [Collecting MRIs with motion artifact](https://discourse.slicer.org/t/collecting-mris-with-motion-artifact/24999)

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**Author:** [@WeitingMD](https://discourse.slicer.org/u/WeitingMD)\
**Replies:** 0\
**Last updated:** [August 30, 2022, 1:04pm UTC](https://discourse.slicer.org/t/collecting-mris-with-motion-artifact/24999 "2022-08-30T13:04:54Z")

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Hi, I am a medical doctor from the University of Toronto and my research team is currently looking for 5000-10000 MRI images with motion artifact. We can purchase the database if necessary. Please email xiongweiting97@g…

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## [Normalisation or scaling with SPHARM](https://discourse.slicer.org/t/normalisation-or-scaling-with-spharm/23602)

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**Author:** [@Khalid\_Saifullah](https://discourse.slicer.org/u/Khalid_Saifullah)\
**Replies:** 9\
**Last updated:** [August 30, 2022, 7:05am UTC](https://discourse.slicer.org/t/normalisation-or-scaling-with-spharm/23602 "2022-08-30T07:05:26Z")

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Hi, I would like to normalise all of my SPHARM-PDM output subjects (subjectID\_pp\_surf\_SPHARM\_procalign.vtk) by a scale factor before running any sort of statistical analysis. I am going to use a separate tool for the st…

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## [How to link link a MarkUp point list to be a sequence in one SequenceBrowser using python script?](https://discourse.slicer.org/t/how-to-link-link-a-markup-point-list-to-be-a-sequence-in-one-sequencebrowser-using-python-script/24951)

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**Author:** [@sunshine](https://discourse.slicer.org/u/sunshine)\
**Replies:** 9\
**Last updated:** [August 30, 2022, 3:51am UTC](https://discourse.slicer.org/t/how-to-link-link-a-markup-point-list-to-be-a-sequence-in-one-sequencebrowser-using-python-script/24951 "2022-08-30T03:51:31Z")

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Hi everyone, I am trying to write a module that can manually add landmarks using the MarkUp point list (vtkMRMLMarkupsFiducialNode) to different SequenceBrowsers. I hope to link the point list node to one sequence of t…

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## [Question regarding converting a model back to a segmentation node](https://discourse.slicer.org/t/question-regarding-converting-a-model-back-to-a-segmentation-node/24974)

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**Author:** [@jegberink](https://discourse.slicer.org/u/jegberink)\
**Replies:** 2\
**Last updated:** [August 29, 2022, 6:52pm UTC](https://discourse.slicer.org/t/question-regarding-converting-a-model-back-to-a-segmentation-node/24974 "2022-08-29T18:52:46Z")

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Hello, My question pertains to the conversion of a model back to a segmentation. Currently i want to overlay 2 CT scans to calculate the dice score between 2 femoral segmentations (preoperative and postoperative). The…

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## [3D slicer for MAC cannot install slicer extensions from files](https://discourse.slicer.org/t/3d-slicer-for-mac-cannot-install-slicer-extensions-from-files/24972)

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**Author:** [@shai-ikko](https://discourse.slicer.org/u/shai-ikko)\
**Replies:** 1\
**Last updated:** [August 29, 2022, 3:12pm UTC](https://discourse.slicer.org/t/3d-slicer-for-mac-cannot-install-slicer-extensions-from-files/24972 "2022-08-29T15:12:27Z")

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Hi, I am developing a pure-python extension of Slicer. It is, at this point, private, so I cannot distribute it through the general extension server, and I have distributed it internally as a zip file. Most users are on…

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## [Whitematteranalysis install on Ubuntu20.02 errors](https://discourse.slicer.org/t/whitematteranalysis-install-on-ubuntu20-02-errors/24977)

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**Author:** [@mxd](https://discourse.slicer.org/u/mxd)\
**Replies:** 0\
**Last updated:** [August 29, 2022, 1:41pm UTC](https://discourse.slicer.org/t/whitematteranalysis-install-on-ubuntu20-02-errors/24977 "2022-08-29T13:41:06Z")

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I am on Ubuntu 20.02 system and following the slicer DMRI tutorial , the White MatterAnalysis successfully built, but when I run \>wm\_quality\_control\_tractyography.py --help, I get errors; Successfully built WhiteMatter…

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## [ShapePopulationViewer](https://discourse.slicer.org/t/shapepopulationviewer/24947)

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**Author:** [@jegberink](https://discourse.slicer.org/u/jegberink)\
**Replies:** 3\
**Last updated:** [August 29, 2022, 12:24pm UTC](https://discourse.slicer.org/t/shapepopulationviewer/24947 "2022-08-29T12:24:45Z")

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Operating system: Windows 10 Slicer version: 5.0.3 Hello, ShapePopulationViewer does not seem to be working for me on 2 different pc’s. On one system Slicer will crash, on the other system it just won’t load and i hav…

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## [Segementation mask file (.nii format) convert .stl format](https://discourse.slicer.org/t/segementation-mask-file-nii-format-convert-stl-format/24971)

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**Author:** [@wawa](https://discourse.slicer.org/u/wawa)\
**Replies:** 0\
**Last updated:** [August 29, 2022, 7:02am UTC](https://discourse.slicer.org/t/segementation-mask-file-nii-format-convert-stl-format/24971 "2022-08-29T07:02:23Z")

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Hi, I am able to convert my data ‘.nii’ Segementation mask files to Model ‘.stl’ files. Segementation mask files is for 3D medical images,which consists of multiple 2D slices. My Code nii\_pathname = ... seg = sli…

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## [When (what kind of circumstance) there can be more than 1 NodeReference with the same ReferenceRole?](https://discourse.slicer.org/t/when-what-kind-of-circumstance-there-can-be-more-than-1-nodereference-with-the-same-referencerole/24964)

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**Author:** [@sunshine](https://discourse.slicer.org/u/sunshine)\
**Replies:** 2\
**Last updated:** [August 29, 2022, 3:59am UTC](https://discourse.slicer.org/t/when-what-kind-of-circumstance-there-can-be-more-than-1-nodereference-with-the-same-referencerole/24964 "2022-08-29T03:59:35Z")

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Hi everyone, I got confused when requiring a node using ReferenceRole. As far as I know about the scene file, one NodeReferenceRole seems to appear only once in a node description. How can we add the 2nd NodeReference …

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## [How to get mouse IJK coordinates?](https://discourse.slicer.org/t/how-to-get-mouse-ijk-coordinates/24968)

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**Author:** [@sunshine](https://discourse.slicer.org/u/sunshine)\
**Replies:** 1\
**Last updated:** [August 29, 2022, 3:44am UTC](https://discourse.slicer.org/t/how-to-get-mouse-ijk-coordinates/24968 "2022-08-29T03:44:46Z")

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Hi everyone, I am trying to write my first module using MarkUp PointList. And I would like to use a label in UI to show the real-time mouse position, both RAS and IJK, just like the screenshot below. I found the RAS…

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## [SUV conversion error - Can't find tag 18 1072 - but tag 18 1078 available](https://discourse.slicer.org/t/suv-conversion-error-cant-find-tag-18-1072-but-tag-18-1078-available/24962)

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**Author:** [@samcyc](https://discourse.slicer.org/u/samcyc)\
**Replies:** 1\
**Last updated:** [August 28, 2022, 7:49pm UTC](https://discourse.slicer.org/t/suv-conversion-error-cant-find-tag-18-1072-but-tag-18-1078-available/24962 "2022-08-28T19:49:33Z")

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Hello everybody, I can’t convert my DICOM files in Bq/mL into SUV. I think the problem comes from the metadata of my data which do not contain the tag (0018,1072) RadiopharmaceuticalStartTime, as the error message of t…

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## [How to understand the difference among (or when to use) getNode byName(), byRenferenceRole(), byID()?](https://discourse.slicer.org/t/how-to-understand-the-difference-among-or-when-to-use-getnode-byname-byrenferencerole-byid/24956)

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**Author:** [@sunshine](https://discourse.slicer.org/u/sunshine)\
**Replies:** 4\
**Last updated:** [August 28, 2022, 7:28pm UTC](https://discourse.slicer.org/t/how-to-understand-the-difference-among-or-when-to-use-getnode-byname-byrenferencerole-byid/24956 "2022-08-28T19:28:34Z")

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Hi everyone, I am trying to write my first extension module, however, really confused by the various methods to get a node: self.\_parameterNode.GetNodeReference('InputVolume') slicer.mrmlScene.GetNodeByID() slicer.util…

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## [How to send transform data from 3D Slicer(Server) to 3D slicer(client) use openIGTLink like Tracking Simulator?](https://discourse.slicer.org/t/how-to-send-transform-data-from-3d-slicer-server-to-3d-slicer-client-use-openigtlink-like-tracking-simulator/24958)

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**Author:** [@xiaosnowqiang](https://discourse.slicer.org/u/xiaosnowqiang)\
**Replies:** 1\
**Last updated:** [August 28, 2022, 11:01am UTC](https://discourse.slicer.org/t/how-to-send-transform-data-from-3d-slicer-server-to-3d-slicer-client-use-openigtlink-like-tracking-simulator/24958 "2022-08-28T11:01:08Z")

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Hello guys,I want use 3D Slicer with the Transforms module as server send data to another 3D Slicer (client), the connect network is OK ,but i don’t know how to send my Transforms module data to another slicer Volume Re…

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## [Matlab Bridge - module execution error - output list of fiducial points](https://discourse.slicer.org/t/matlab-bridge-module-execution-error-output-list-of-fiducial-points/8407)

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**Author:** [@marlene](https://discourse.slicer.org/u/marlene)\
**Replies:** 10\
**Last updated:** [December 10, 2020, 1:10am UTC](https://discourse.slicer.org/t/matlab-bridge-module-execution-error-output-list-of-fiducial-points/8407 "2020-12-10T01:10:56Z")

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Operating system:Ubuntu 16.04 Slicer version: 4.10 Expected behavior: output fiducial from Matlab Bridge extension Actual behavior: error Hello everybody, I am implementing a Matlab Bridge extension which takes as in…

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## [CreateDefaultVolumeRenderingNodes always return None](https://discourse.slicer.org/t/createdefaultvolumerenderingnodes-always-return-none/24932)

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**Author:** [@ada](https://discourse.slicer.org/u/ada)\
**Replies:** 1\
**Last updated:** [August 27, 2022, 10:49pm UTC](https://discourse.slicer.org/t/createdefaultvolumerenderingnodes-always-return-none/24932 "2022-08-27T22:49:35Z")

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Hello community! I was using a custom script to display 3D dicom stacks but since I updated 3DSlicer version (from 4.11.0 to 5.0.3) my script is not working anymore. I am no more able to get the ROI node from a volume …

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## [mrc file- reading error ](https://discourse.slicer.org/t/mrc-file-reading-error/24952)

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**Author:** [@deniseYR](https://discourse.slicer.org/u/deniseYR)\
**Replies:** 1\
**Last updated:** [August 27, 2022, 10:08pm UTC](https://discourse.slicer.org/t/mrc-file-reading-error/24952 "2022-08-27T22:08:18Z")

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Hi all. I am trying to load 4 different volume files of some micro CT scans I did, but every time I try to open them in 3D slicer I get an error message that says the following: Error occurred while loading the selected…

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## [Using the Slicer for preoperative planning measurements in CT based 3D models of Bones](https://discourse.slicer.org/t/using-the-slicer-for-preoperative-planning-measurements-in-ct-based-3d-models-of-bones/24954)

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**Author:** [@Nele](https://discourse.slicer.org/u/Nele)\
**Replies:** 1\
**Last updated:** [August 27, 2022, 10:02pm UTC](https://discourse.slicer.org/t/using-the-slicer-for-preoperative-planning-measurements-in-ct-based-3d-models-of-bones/24954 "2022-08-27T22:02:45Z")

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Operating system: MacOS Can I sue the Slicer for preoperative planning purposes - specifically angle measurements in CT based 3D models of Bones?

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## [Collision detection between not polyhedron models](https://discourse.slicer.org/t/collision-detection-between-not-polyhedron-models/24948)

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**Author:** [@mosenco](https://discourse.slicer.org/u/mosenco)\
**Replies:** 1\
**Last updated:** [August 27, 2022, 9:53pm UTC](https://discourse.slicer.org/t/collision-detection-between-not-polyhedron-models/24948 "2022-08-27T21:53:11Z")

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i’ve been following this guide and implemented into my code and it doesnt work. I have a white and pial file, from freesurfer that are models that represent the white and pial surface of the brain. I have also multiple…

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## [Renaming fiducial control points in the slice view window](https://discourse.slicer.org/t/renaming-fiducial-control-points-in-the-slice-view-window/24922)

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**Author:** [@AMK](https://discourse.slicer.org/u/AMK)\
**Replies:** 1\
**Last updated:** [August 26, 2022, 9:08pm UTC](https://discourse.slicer.org/t/renaming-fiducial-control-points-in-the-slice-view-window/24922 "2022-08-26T21:08:42Z")

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Hi, I am trying to automate the naming of the fiducial control points in the slice view window. The user selects the markup points. Now, I am able to rename the points in the data module. But the name remains the same i…

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## [Local threshold : mouse cursor is never restored](https://discourse.slicer.org/t/local-threshold-mouse-cursor-is-never-restored/24941)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 1\
**Last updated:** [August 26, 2022, 8:35pm UTC](https://discourse.slicer.org/t/local-threshold-mouse-cursor-is-never-restored/24941 "2022-08-26T20:35:42Z")

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‘Local threshold’ segment editor effect outputs the following in Python console : Traceback (most recent call last): File "/home/user/programs/Slicer/bin/../lib/Slicer-5.1/qt-scripted-modules/SegmentEditorLocalThresho…

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