# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?no_subcategories=false&page=12

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

**Page:** 13

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## [Smoothen NIFTI file](https://discourse.slicer.org/t/smoothen-nifti-file/40281)

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**Author:** [@Amine\_MK](https://discourse.slicer.org/u/Amine_MK)\
**Replies:** 1\
**Last updated:** [November 20, 2024, 9:52pm UTC](https://discourse.slicer.org/t/smoothen-nifti-file/40281 "2024-11-20T21:52:22Z")

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Hello I noticed that when we open a NIFTI file in Slicer, it automatically applies a transformation to the mesh and make it smooth. I would like to know if we can access this feature through Python code? And what is the…

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## [Select specific control points from qSlicerSimpleMarkupsWidget](https://discourse.slicer.org/t/select-specific-control-points-from-qslicersimplemarkupswidget/40270)

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**Author:** [@justomont](https://discourse.slicer.org/u/justomont)\
**Replies:** 0\
**Last updated:** [November 19, 2024, 5:30pm UTC](https://discourse.slicer.org/t/select-specific-control-points-from-qslicersimplemarkupswidget/40270 "2024-11-19T17:30:48Z")

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Hey there! I’m developing a scripted module and I want the user to be able to select and unselect specific markup control points from the module’s GUI, similarly to what can be done from the Markups module. For example,…

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## [Mask Volume Logic](https://discourse.slicer.org/t/mask-volume-logic/40235)

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**Author:** [@Filippo\_Parronchi](https://discourse.slicer.org/u/Filippo_Parronchi)\
**Replies:** 1\
**Last updated:** [November 18, 2024, 9:31pm UTC](https://discourse.slicer.org/t/mask-volume-logic/40235 "2024-11-18T21:31:59Z")

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Hi everyone, I’m using a 3D Slicer instance without GUI (headless representation) on my Apache2 server. In my Python script, I can’t use the widget representation, so I need to directly call the logic functions of the…

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## [Extracting transformation matrix information from needle models overlaid on ultrasound images](https://discourse.slicer.org/t/extracting-transformation-matrix-information-from-needle-models-overlaid-on-ultrasound-images/40255)

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**Author:** [@Sangrok](https://discourse.slicer.org/u/Sangrok)\
**Replies:** 0\
**Last updated:** [November 18, 2024, 9:00pm UTC](https://discourse.slicer.org/t/extracting-transformation-matrix-information-from-needle-models-overlaid-on-ultrasound-images/40255 "2024-11-18T21:00:13Z")

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Hello. Using 3D Slicer, I implemented the registration of ultrasound images and OTS data, overlaying a cyan-colored needle model on the ultrasound images. As shown in the figure below, I want to extract the needle tip p…

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## [A corner-case issue with invoking CLI modules](https://discourse.slicer.org/t/a-corner-case-issue-with-invoking-cli-modules/40246)

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**Author:** [@shai-ikko](https://discourse.slicer.org/u/shai-ikko)\
**Replies:** 0\
**Last updated:** [November 18, 2024, 4:37pm UTC](https://discourse.slicer.org/t/a-corner-case-issue-with-invoking-cli-modules/40246 "2024-11-18T16:37:38Z")

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Hi, TL;DR: There’s a little clash between Slicer CLI module invocation and Python’s argparse, in a corner case; there’s a non-obvious workaround; maybe there should be a fix. I’m developing some functionality in Slicer…

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## [Use Class from Main Python Script in a python file in subfolder](https://discourse.slicer.org/t/use-class-from-main-python-script-in-a-python-file-in-subfolder/40074)

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**Author:** [@maximeb](https://discourse.slicer.org/u/maximeb)\
**Replies:** 2\
**Last updated:** [November 18, 2024, 3:34pm UTC](https://discourse.slicer.org/t/use-class-from-main-python-script-in-a-python-file-in-subfolder/40074 "2024-11-18T15:34:14Z")

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Hi, Our team is developing a Slicer module. We want to split our code into different python files (are in subfolders). It works to import variables and functions (for example) from modules to main, but when we try to i…

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## ["Surface Smoothing" in Volume Rendering - Sparkling Artifacts on Rendered Images](https://discourse.slicer.org/t/surface-smoothing-in-volume-rendering-sparkling-artifacts-on-rendered-images/40238)

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**Author:** [@park](https://discourse.slicer.org/u/park)\
**Replies:** 0\
**Last updated:** [November 18, 2024, 4:07am UTC](https://discourse.slicer.org/t/surface-smoothing-in-volume-rendering-sparkling-artifacts-on-rendered-images/40238 "2024-11-18T04:07:25Z")

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Hi all, I’ve been working with volume rendering, specifically using the “Surface Smoothing” feature. However, I noticed that enabling this feature introduces sparkling artifacts on the rendered images, as shown in the a…

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## [SlicerRT build fails with new DCMTK](https://discourse.slicer.org/t/slicerrt-build-fails-with-new-dcmtk/40177)

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**Author:** [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Replies:** 14\
**Last updated:** [November 16, 2024, 2:58pm UTC](https://discourse.slicer.org/t/slicerrt-build-fails-with-new-dcmtk/40177 "2024-11-16T14:58:05Z")

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Just posting this quickly in case someone knows this off the top off their head. I noticed lately that DCMTK probably changed under Slicer. Unfortunately besides some inconveniences (like having to do a clean build of S…

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## [Asynchronous design pattern](https://discourse.slicer.org/t/asynchronous-design-pattern/40159)

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**Author:** [@JASON](https://discourse.slicer.org/u/JASON)\
**Replies:** 3\
**Last updated:** [November 15, 2024, 9:58pm UTC](https://discourse.slicer.org/t/asynchronous-design-pattern/40159 "2024-11-15T21:58:31Z")

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Hello, I am developing UI for a few tasks in 3D Slicer that take a while to execute (remote database query, or some local compute task). What are some common design patterns for handling these tasks in an asynchronous m…

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## [Automatically erase a part of a segmentation](https://discourse.slicer.org/t/automatically-erase-a-part-of-a-segmentation/40218)

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**Author:** [@Fleur\_Gaudfernau](https://discourse.slicer.org/u/Fleur_Gaudfernau)\
**Replies:** 0\
**Last updated:** [November 15, 2024, 4:11pm UTC](https://discourse.slicer.org/t/automatically-erase-a-part-of-a-segmentation/40218 "2024-11-15T16:11:15Z")

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Hello, I am fairly new to using python scripts in Slicer. I have rather simple brain segmentation (1 label) and I want to physically separate the brain hemispheres, i.e. remove the junction between the hemispheres and …

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## [Creating a module for electron bolus](https://discourse.slicer.org/t/creating-a-module-for-electron-bolus/37766)

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**Author:** [@sima](https://discourse.slicer.org/u/sima)\
**Replies:** 38\
**Last updated:** [November 15, 2024, 8:46am UTC](https://discourse.slicer.org/t/creating-a-module-for-electron-bolus/37766 "2024-11-15T08:46:53Z")

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Hi professors I manually designed individual electron bolus using 3D slicer software for my thesis a year ago. Now I have written Python codes to have electron bolus in 3D slicer automatically. and I am eager to add th…

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## [How to Disable Right-Click Context Menu in Toolbar Area?](https://discourse.slicer.org/t/how-to-disable-right-click-context-menu-in-toolbar-area/40197)

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**Author:** [@nih4t](https://discourse.slicer.org/u/nih4t)\
**Replies:** 0\
**Last updated:** [November 14, 2024, 2:37pm UTC](https://discourse.slicer.org/t/how-to-disable-right-click-context-menu-in-toolbar-area/40197 "2024-11-14T14:37:06Z")

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Hello, I am working on a custom 3D Slicer application and would like to disable the right-click functionality in the toolbar area, next to the data load button (see attached image for reference). Is there a way to compl…

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## [There was an issue when running ./Slicer --launch /home/xxx/Qt5.14.2/Tools/QtCreator/bin/qtcreator on Ubuntu 18.04.](https://discourse.slicer.org/t/there-was-an-issue-when-running-slicer-launch-home-xxx-qt5-14-2-tools-qtcreator-bin-qtcreator-on-ubuntu-18-04/40173)

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**Author:** [@tthh7](https://discourse.slicer.org/u/tthh7)\
**Replies:** 2\
**Last updated:** [November 14, 2024, 1:17am UTC](https://discourse.slicer.org/t/there-was-an-issue-when-running-slicer-launch-home-xxx-qt5-14-2-tools-qtcreator-bin-qtcreator-on-ubuntu-18-04/40173 "2024-11-14T01:17:39Z")

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I successfully built Slicer version 5.7.0-2024-11-08 on Ubuntu 18.04 following the instructions in the Slicer documentation. However, when I try to debug using Qt, I run into an issue. I launched Qt Creator using the com…

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## [Issue with Cursor RAS Position Retrieval in Slicer 5.7](https://discourse.slicer.org/t/issue-with-cursor-ras-position-retrieval-in-slicer-5-7/40064)

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**Author:** [@park](https://discourse.slicer.org/u/park)\
**Replies:** 3\
**Last updated:** [November 12, 2024, 7:33pm UTC](https://discourse.slicer.org/t/issue-with-cursor-ras-position-retrieval-in-slicer-5-7/40064 "2024-11-12T19:33:17Z")

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Hi all, I’m trying to retrieve the cursor’s RAS position using the following code: ras = \[0, 0, 0\] crosshairNode.GetCursorPositionRAS(ras) In Slicer 5.6, when the cursor was positioned over the modelNode, it would ret…

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## [Persistent favorites folder in Add Data GUI](https://discourse.slicer.org/t/persistent-favorites-folder-in-add-data-gui/21595)

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**Author:** [@phcerdan](https://discourse.slicer.org/u/phcerdan)\
**Replies:** 14\
**Last updated:** [November 12, 2024, 3:24pm UTC](https://discourse.slicer.org/t/persistent-favorites-folder-in-add-data-gui/21595 "2024-11-12T15:24:27Z")

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Dropping a folder to the list of favorites is great: But it would be even better if it persist after a restart, or at least that there is an option in general settings to set my favorites folders. Another related op…

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## [Run python script in thread cause crash](https://discourse.slicer.org/t/run-python-script-in-thread-cause-crash/40139)

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**Author:** [@fqzhice](https://discourse.slicer.org/u/fqzhice)\
**Replies:** 0\
**Last updated:** [November 12, 2024, 1:42am UTC](https://discourse.slicer.org/t/run-python-script-in-thread-cause-crash/40139 "2024-11-12T01:42:22Z")

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Hi I try to run heavy calculation by qtimer cmd = “pythonSlicerExecutablePath=os.path.dirname(sys.executable)+‘/PythonSlicer.exe’\\n” “commandLine = \[pythonSlicerExecutablePath, script, ‘%1’\]\\n” “proc=slicer.util.lau…

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## [Unexpected interactions of ROI objects with code](https://discourse.slicer.org/t/unexpected-interactions-of-roi-objects-with-code/40053)

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**Author:** [@shai-ikko](https://discourse.slicer.org/u/shai-ikko)\
**Replies:** 4\
**Last updated:** [November 11, 2024, 9:49am UTC](https://discourse.slicer.org/t/unexpected-interactions-of-roi-objects-with-code/40053 "2024-11-11T09:49:55Z")

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This continues the topic Configure ROI to match volume through code but I think that post was not phrased very well, so let’s start again: I’m creating a ROI with code based on an example from the script repository: se…

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## [Help submitting extension Breast DCE-MRI FTV](https://discourse.slicer.org/t/help-submitting-extension-breast-dce-mri-ftv/18955)

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**Author:** [@rohan\_n](https://discourse.slicer.org/u/rohan_n)\
**Replies:** 21\
**Last updated:** [November 9, 2024, 4:38pm UTC](https://discourse.slicer.org/t/help-submitting-extension-breast-dce-mri-ftv/18955 "2024-11-09T16:38:47Z")

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I just submitted pull request for my new extension to the master branch of Extensions Index. The attached image says that 1 of the 3 checks failed. Is this something I need to fix? If so, how? I submitted this pull …

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## [How to Activate Slice View on Mouse Hover](https://discourse.slicer.org/t/how-to-activate-slice-view-on-mouse-hover/39937)

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**Author:** [@huwqchn](https://discourse.slicer.org/u/huwqchn)\
**Replies:** 11\
**Last updated:** [November 1, 2024, 4:59pm UTC](https://discourse.slicer.org/t/how-to-activate-slice-view-on-mouse-hover/39937 "2024-11-01T16:59:28Z")

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Hi everyone, I’ve set up multiple shortcuts for each view, but they only work if I click to activate the view first. I’d like to improve my workflow by activating views on mouse hover instead, so shortcuts are immediate…

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## [Convertion from DICOM to Nifti for multiple dicom series](https://discourse.slicer.org/t/convertion-from-dicom-to-nifti-for-multiple-dicom-series/40067)

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**Author:** [@fabiogatelli](https://discourse.slicer.org/u/fabiogatelli)\
**Replies:** 0\
**Last updated:** [November 7, 2024, 12:34pm UTC](https://discourse.slicer.org/t/convertion-from-dicom-to-nifti-for-multiple-dicom-series/40067 "2024-11-07T12:34:58Z")

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Hi all, I’m trying to perform the DICOM to NIFTI conversion using 3DSlicer for multiple dicom series. I wonder if there is a way to exploit 3DSlicer converter to perform in a more automatic way this conversion. For examp…

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## [How to disable the splash screen before launching the program](https://discourse.slicer.org/t/how-to-disable-the-splash-screen-before-launching-the-program/29928)

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**Author:** [@nnzzll](https://discourse.slicer.org/u/nnzzll)\
**Replies:** 3\
**Last updated:** [November 7, 2024, 5:48am UTC](https://discourse.slicer.org/t/how-to-disable-the-splash-screen-before-launching-the-program/29928 "2024-11-07T05:48:30Z")

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I am developing a custom app of Slicer and I need to setup the splash screen defined by user’s choice. I’ve read this post :change-the-splash-screen-of-slicer-upon-launch, noticed that there are two splash screen during…

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## [Upscale cropped videostream](https://discourse.slicer.org/t/upscale-cropped-videostream/40054)

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**Author:** [@J.vd.Zee](https://discourse.slicer.org/u/J.vd.Zee)\
**Replies:** 0\
**Last updated:** [November 6, 2024, 2:44pm UTC](https://discourse.slicer.org/t/upscale-cropped-videostream/40054 "2024-11-06T14:44:51Z")

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Hi all, In the Plus Server Launcher, videos can be streamed to 3D Slicer. Moreover, within this configuration (i.e., .xml file, mmfVideo, Media Foundation) users can crop the incoming video stream by the ClipRectangle… …

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## [Image calculator](https://discourse.slicer.org/t/image-calculator/40035)

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**Author:** [@ashkanpakzad](https://discourse.slicer.org/u/ashkanpakzad)\
**Replies:** 3\
**Last updated:** [November 5, 2024, 11:45pm UTC](https://discourse.slicer.org/t/image-calculator/40035 "2024-11-05T23:45:34Z")

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Hi all, My first post, thanks for all the good work. I’m keen to get involved. I was wondering if anyone has developed in Slicer something like ImageJ/FIJI’s ‘image calculator’? Which would allow the user to manipu…

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## [Control point modified event is not fired](https://discourse.slicer.org/t/control-point-modified-event-is-not-fired/39783)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 5\
**Last updated:** [November 5, 2024, 2:38pm UTC](https://discourse.slicer.org/t/control-point-modified-event-is-not-fired/39783 "2024-11-05T14:38:35Z")

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Hi, I think I’ve found a bug: lineNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLMarkupsLineNode") slicer.mrmlScene.AddNode(lineNode) slicer.modules.markups.logic().AddNewDisplayNodeForMarkupsNode(lineNode) lineNode…

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## [Volume rendering file shows up as changed in Save dialog directly after opening an mrml scene](https://discourse.slicer.org/t/volume-rendering-file-shows-up-as-changed-in-save-dialog-directly-after-opening-an-mrml-scene/39979)

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**Author:** [@MMMPPPMMM](https://discourse.slicer.org/u/MMMPPPMMM)\
**Replies:** 3\
**Last updated:** [November 4, 2024, 10:49pm UTC](https://discourse.slicer.org/t/volume-rendering-file-shows-up-as-changed-in-save-dialog-directly-after-opening-an-mrml-scene/39979 "2024-11-04T22:49:11Z")

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Hello It seems to me like a bug that the \*.vp volume rendering file shows up as changed in Save dialog directly after opening an MRML scene? Find an example here: Upload Files | Free File Upload and Transfer Up To 10 G…

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## [ Further Simplifying a Custom 3D Slicer Application: Removing Unneeded Modules and Adding Custom Modules](https://discourse.slicer.org/t/further-simplifying-a-custom-3d-slicer-application-removing-unneeded-modules-and-adding-custom-modules/40025)

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**Author:** [@nih4t](https://discourse.slicer.org/u/nih4t)\
**Replies:** 0\
**Last updated:** [November 4, 2024, 10:48pm UTC](https://discourse.slicer.org/t/further-simplifying-a-custom-3d-slicer-application-removing-unneeded-modules-and-adding-custom-modules/40025 "2024-11-04T22:48:58Z")

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Hello, I’ve successfully built a simplified version of 3D Slicer following this guide from Kitware (https://www.kitware.com/slicercat-creating-custom-applications-based-on-3d-slicer/). Hello, I’ve successfully built a…

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## [For qMRMLNodeComboBox, how can I restrict Sequence nodes by type?](https://discourse.slicer.org/t/for-qmrmlnodecombobox-how-can-i-restrict-sequence-nodes-by-type/39959)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 3\
**Last updated:** [November 1, 2024, 8:18pm UTC](https://discourse.slicer.org/t/for-qmrmlnodecombobox-how-can-i-restrict-sequence-nodes-by-type/39959 "2024-11-01T20:18:41Z")

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I am working on a module to process a 4D data set. It will need to take as inputs a sequence node of segmentations and a sequence node of tables. Also present in the scene will be (possibly multple) sequence nodes of i…

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## [Markup control point coordinate values are not automatically updated when switching between World and Local](https://discourse.slicer.org/t/markup-control-point-coordinate-values-are-not-automatically-updated-when-switching-between-world-and-local/39982)

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**Author:** [@MMMPPPMMM](https://discourse.slicer.org/u/MMMPPPMMM)\
**Replies:** 1\
**Last updated:** [November 1, 2024, 3:02pm UTC](https://discourse.slicer.org/t/markup-control-point-coordinate-values-are-not-automatically-updated-when-switching-between-world-and-local/39982 "2024-11-01T15:02:57Z")

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Hello When I switch between “World” and “Local” in the “Coordinates:” drop down list of the Control Points section of the Markups module, the coordinates are not automatically updated. As workaround one can use the “Pr…

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## [Two markupsROI (Cropping module)](https://discourse.slicer.org/t/two-markupsroi-cropping-module/39956)

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**Author:** [@Dawid\_Szczawinski](https://discourse.slicer.org/u/Dawid_Szczawinski)\
**Replies:** 2\
**Last updated:** [October 31, 2024, 4:24pm UTC](https://discourse.slicer.org/t/two-markupsroi-cropping-module/39956 "2024-10-31T16:24:46Z")

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Hello everyone! I try to create my own extension to using nnunetv2 model. First step is cropping data, because segmentation full file is not necessary and I have too little ram. So I try to cropp Volume using ROI. Is…

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## [How to elicit a ray and tangent to the ROI region (use a python script if possible)](https://discourse.slicer.org/t/how-to-elicit-a-ray-and-tangent-to-the-roi-region-use-a-python-script-if-possible/39954)

<div class="topic-metadata">

**Author:** [@hewanglan](https://discourse.slicer.org/u/hewanglan)\
**Replies:** 2\
**Last updated:** [October 31, 2024, 11:55am UTC](https://discourse.slicer.org/t/how-to-elicit-a-ray-and-tangent-to-the-roi-region-use-a-python-script-if-possible/39954 "2024-10-31T11:55:51Z")

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Operating system:windows 64 bit Slicer version:5.7.0 Expected behavior: Actual behavior:

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