# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?no_subcategories=false&page=55

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

**Page:** 56

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## [\[Linux\] SliceOpenCV build](https://discourse.slicer.org/t/linux-sliceopencv-build/23269)

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**Author:** [@adamrankin](https://discourse.slicer.org/u/adamrankin)\
**Replies:** 2\
**Last updated:** [May 5, 2022, 2:58pm UTC](https://discourse.slicer.org/t/linux-sliceopencv-build/23269 "2022-05-05T14:58:37Z")

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I am trying to fix the SlicerOpenCV build in order to re-enable the extension, but I am experiencing some roadblocks. I am able to successfully build the extension on Ubuntu 20.04 with gcc 9.x. I notice that the build m…

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## [Center coordinates of volume slices?](https://discourse.slicer.org/t/center-coordinates-of-volume-slices/23133)

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**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 7\
**Last updated:** [May 4, 2022, 3:57pm UTC](https://discourse.slicer.org/t/center-coordinates-of-volume-slices/23133 "2022-05-04T15:57:40Z")

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How do I get the center coordinates for a volume that is shifted to the left and zoomed in a bit during maniplations? Example: from to I am interested in the screen coordinates. Thanks.

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## [Help for package testing on macOS Monterrey or BigSur system](https://discourse.slicer.org/t/help-for-package-testing-on-macos-monterrey-or-bigsur-system/23249)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 9\
**Last updated:** [May 4, 2022, 2:31pm UTC](https://discourse.slicer.org/t/help-for-package-testing-on-macos-monterrey-or-bigsur-system/23249 "2022-05-04T14:31:01Z")

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Context To perform some testing to check if issue Slicer#6347 reported by @che85 is specific to recent macOS system or if it is related to specific network & proxy settings. Help needed Two ways you could help: Reach…

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## [SlicerHeart compiling](https://discourse.slicer.org/t/slicerheart-compiling/23191)

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**Author:** [@whu](https://discourse.slicer.org/u/whu)\
**Replies:** 6\
**Last updated:** [May 4, 2022, 1:02pm UTC](https://discourse.slicer.org/t/slicerheart-compiling/23191 "2022-05-04T13:02:03Z")

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who can share the experience of building SlicerHeart from source ? 1)strange error CMake Error at xx/SlicerHeart-build/ITKStrain-prefix/tmp/ITKStrain-gitupdate.cmake:97 (execute\_process): 2\> execute\_process failed c…

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## [\[Volume Rendering\] Works via python console but not via extension code](https://discourse.slicer.org/t/volume-rendering-works-via-python-console-but-not-via-extension-code/23248)

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**Author:** [@strider\_hunter](https://discourse.slicer.org/u/strider_hunter)\
**Replies:** 2\
**Last updated:** [May 4, 2022, 7:58am UTC](https://discourse.slicer.org/t/volume-rendering-works-via-python-console-but-not-via-extension-code/23248 "2022-05-04T07:58:42Z")

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Hi, When I use the following code in my Slicer Extension (Slicer 4.11.20210226), I am unable to get a volume render in the 3D view (a custom vtkMRMLViewNode). node = slicer.util.getNode('\<nodename\>') # a vtkMRMLScalarV…

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## [Build process failed with errors](https://discourse.slicer.org/t/build-process-failed-with-errors/23114)

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**Author:** [@Mrwa\_Awoda](https://discourse.slicer.org/u/Mrwa_Awoda)\
**Replies:** 5\
**Last updated:** [May 3, 2022, 9:42pm UTC](https://discourse.slicer.org/t/build-process-failed-with-errors/23114 "2022-05-03T21:42:18Z")

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My op-system is Windows 10. Qt5.15.2 CMake version 3.22.2 Visual Studio 17 2022 I’m having errors with the Slicer build process in Release mode. Some errors such as (Error File C:/D/S4R/SimpleITK/CMake/CTestCustom.c…

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## [Update related to available CDash projects](https://discourse.slicer.org/t/update-related-to-available-cdash-projects/23252)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 0\
**Last updated:** [May 3, 2022, 6:23am UTC](https://discourse.slicer.org/t/update-related-to-available-cdash-projects/23252 "2022-05-03T06:23:24Z")

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As originally discussed in hangout from 2019-03-26, and later tracked in issue #4644, build reports associated with Stable and Preview builds are submitted to dedicated CDash projects hosted at https://slicer.cdash.org: …

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## [Loadable custom markups : how to install the packaged extension](https://discourse.slicer.org/t/loadable-custom-markups-how-to-install-the-packaged-extension/23238)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 1\
**Last updated:** [May 2, 2022, 5:22pm UTC](https://discourse.slicer.org/t/loadable-custom-markups-how-to-install-the-packaged-extension/23238 "2022-05-02T17:22:45Z")

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I’m in the very early stages trying to create a loadable custom markups in C++, using extension wizard’s template. I can build the extension and module outside Slicer’s build tree, and create an extension package. When…

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## [How to clip a model from a volume node through a ROI without the crop Volume?](https://discourse.slicer.org/t/how-to-clip-a-model-from-a-volume-node-through-a-roi-without-the-crop-volume/23210)

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**Author:** [@jumbojing](https://discourse.slicer.org/u/jumbojing)\
**Replies:** 0\
**Last updated:** [May 1, 2022, 2:35am UTC](https://discourse.slicer.org/t/how-to-clip-a-model-from-a-volume-node-through-a-roi-without-the-crop-volume/23210 "2022-05-01T02:35:41Z")

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How to clip a model from a volume node through a ROI without the crop Volume? or with some faster ways?

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## [Developing slicer applications with different GUI interfaces based on slicer](https://discourse.slicer.org/t/developing-slicer-applications-with-different-gui-interfaces-based-on-slicer/23189)

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**Author:** [@zhiyuan](https://discourse.slicer.org/u/zhiyuan)\
**Replies:** 4\
**Last updated:** [April 29, 2022, 1:03pm UTC](https://discourse.slicer.org/t/developing-slicer-applications-with-different-gui-interfaces-based-on-slicer/23189 "2022-04-29T13:03:39Z")

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I am a graduate student from China who studies biomedical image processing. Recently, I have a research project that needs to cut the surface of the segmented 3D medical image, which can just use some functions of 3D sli…

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## [Saved dicom to nii with saveNode, changes range of intensities and image volume](https://discourse.slicer.org/t/saved-dicom-to-nii-with-savenode-changes-range-of-intensities-and-image-volume/23094)

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**Author:** [@S\_Arbabi](https://discourse.slicer.org/u/S_Arbabi)\
**Replies:** 3\
**Last updated:** [April 28, 2022, 5:11pm UTC](https://discourse.slicer.org/t/saved-dicom-to-nii-with-savenode-changes-range-of-intensities-and-image-volume/23094 "2022-04-28T17:11:31Z")

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Hi, I load a dicom series and save it as nrrd like this: img\_node = DiskSimulator.load\_image(img\_dcm\_dir, iid) slicer.util.saveNode(img\_node, os.path.join(self.imgs\_nii\_dir, iid, f"{iid}.nii.gz")) where load\_image met…

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## [Segmentation using thresholding using Python](https://discourse.slicer.org/t/segmentation-using-thresholding-using-python/7833)

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**Author:** [@jazlynn21100](https://discourse.slicer.org/u/jazlynn21100)\
**Replies:** 18\
**Last updated:** [April 27, 2022, 3:02pm UTC](https://discourse.slicer.org/t/segmentation-using-thresholding-using-python/7833 "2022-04-27T15:02:33Z")

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## [Instructions/Advice for adding ThresholdMaximumConnectedComponentsImageFilter or AutomaticThresholdImageFilter as a segment editor effect](https://discourse.slicer.org/t/instructions-advice-for-adding-thresholdmaximumconnectedcomponentsimagefilter-or-automaticthresholdimagefilter-as-a-segment-editor-effect/23124)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 1\
**Last updated:** [April 26, 2022, 12:23pm UTC](https://discourse.slicer.org/t/instructions-advice-for-adding-thresholdmaximumconnectedcomponentsimagefilter-or-automaticthresholdimagefilter-as-a-segment-editor-effect/23124 "2022-04-26T12:23:36Z")

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I’m interested in using this filter since it allows to get the threshold value that maximizes the number of islands in an image. I want to use this value as input for another filter. So I was thinking in adding this filt…

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## [ScreenShot is toooo small when red/yellow/green view too small](https://discourse.slicer.org/t/screenshot-is-toooo-small-when-red-yellow-green-view-too-small/23110)

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**Author:** [@caiqj1203](https://discourse.slicer.org/u/caiqj1203)\
**Replies:** 3\
**Last updated:** [April 26, 2022, 3:10am UTC](https://discourse.slicer.org/t/screenshot-is-toooo-small-when-red-yellow-green-view-too-small/23110 "2022-04-26T03:10:11Z")

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I resize main window like this . and I use captureImageFromView function to generate screenshot, the screenshot like this What can I do to make the size of the screenshot independent of the display window?

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## [Modify value in \`SlicerLauncherSettings.ini\` from application](https://discourse.slicer.org/t/modify-value-in-slicerlaunchersettings-ini-from-application/23000)

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**Author:** [@keri](https://discourse.slicer.org/u/keri)\
**Replies:** 5\
**Last updated:** [April 25, 2022, 12:56pm UTC](https://discourse.slicer.org/t/modify-value-in-slicerlaunchersettings-ini-from-application/23000 "2022-04-25T12:56:17Z")

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Hi, Is it possible to set value to SlicerLauncherSettings.ini from application? For example: slicer.app.setEnvironmentVariable("SLICER\_HOME", "/my/path") will modify SLICER\_HOME env var but it doesn’t change the valu…

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## [Slicer crashing when using multiprocessing or multi threading](https://discourse.slicer.org/t/slicer-crashing-when-using-multiprocessing-or-multi-threading/23095)

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**Author:** [@vanlangk](https://discourse.slicer.org/u/vanlangk)\
**Replies:** 2\
**Last updated:** [April 25, 2022, 1:03am UTC](https://discourse.slicer.org/t/slicer-crashing-when-using-multiprocessing-or-multi-threading/23095 "2022-04-25T01:03:25Z")

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Hi guys, I am currently working on a voice interface for 3D slicer. I’m implementing it using a scripted module for 3d Slicer where it creates a child process, and then continually listens for words from the child proce…

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## [Utilise Slicer GUI when effect/module is running](https://discourse.slicer.org/t/utilise-slicer-gui-when-effect-module-is-running/23065)

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**Author:** [@Karthik](https://discourse.slicer.org/u/Karthik)\
**Replies:** 1\
**Last updated:** [April 21, 2022, 1:48pm UTC](https://discourse.slicer.org/t/utilise-slicer-gui-when-effect-module-is-running/23065 "2022-04-21T13:48:09Z")

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Hi. I have written a segment editor effect. This effect usually takes about 8 minutes to run. However, during this time, Slicer is frozen and hence I cannot use it for anything else. Is it possible to still utilise slic…

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## [How to interpret the GetMTime() output and write an igs.mha file?](https://discourse.slicer.org/t/how-to-interpret-the-getmtime-output-and-write-an-igs-mha-file/22961)

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**Author:** [@Srijeet\_Chatterjee](https://discourse.slicer.org/u/Srijeet_Chatterjee)\
**Replies:** 2\
**Last updated:** [April 21, 2022, 7:59am UTC](https://discourse.slicer.org/t/how-to-interpret-the-getmtime-output-and-write-an-igs-mha-file/22961 "2022-04-21T07:59:22Z")

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Hello everyone, I am trying to use the OpenIGTLink to record frames and use detection algorithms like Aruco. Ideally I should be able to store each transformation matrix every time the frames are updated. I used the Get…

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## [RAS coordinates to Image coordinates](https://discourse.slicer.org/t/ras-coordinates-to-image-coordinates/15019)

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**Author:** [@justomont](https://discourse.slicer.org/u/justomont)\
**Replies:** 3\
**Last updated:** [December 19, 2020, 6:53am UTC](https://discourse.slicer.org/t/ras-coordinates-to-image-coordinates/15019 "2020-12-19T06:53:18Z")

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Operating system: macOS Big Sur 11.0.1 Slicer version: 4.10.1 Dear Developers and Users, I have a lot of fiducial markup points in the RAS Coordinates System, as can be seen in the screen capture, for example X’5 …

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## [Slicer cli starts before the last cli ends](https://discourse.slicer.org/t/slicer-cli-starts-before-the-last-cli-ends/23056)

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**Author:** [@hotsen](https://discourse.slicer.org/u/hotsen)\
**Replies:** 1\
**Last updated:** [April 20, 2022, 5:22pm UTC](https://discourse.slicer.org/t/slicer-cli-starts-before-the-last-cli-ends/23056 "2022-04-20T17:22:32Z")

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Hi all, I got the following issue with slicer.cli.run. The first loop generates 3 registration output volumes, then the second loop extracts features from those 3 output volumes. But the last extraction always went wron…

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## ["All segments" is inconsistent in Segment Editor](https://discourse.slicer.org/t/all-segments-is-inconsistent-in-segment-editor/23051)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 7\
**Last updated:** [April 20, 2022, 4:06pm UTC](https://discourse.slicer.org/t/all-segments-is-inconsistent-in-segment-editor/23051 "2022-04-20T16:06:08Z")

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I’ve been using scissors with “Apply to all segments” to erase or fill in multiple segments. This works on all visible segments, which is actually not what the check box says, but it is what I want it to do, so it works …

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## [Run script when SlicerCAT first time launched](https://discourse.slicer.org/t/run-script-when-slicercat-first-time-launched/22993)

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**Author:** [@keri](https://discourse.slicer.org/u/keri)\
**Replies:** 8\
**Last updated:** [April 18, 2022, 1:40pm UTC](https://discourse.slicer.org/t/run-script-when-slicercat-first-time-launched/22993 "2022-04-18T13:40:57Z")

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Hi, I need to do some customizations when user first time launches SlicerCAT. Is there a way to achieve that? More detailly: I bundle julia with SlicerCAT. I install some packages to julia during buildtime but these…

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## [Migrate the 3D slicer to my own program](https://discourse.slicer.org/t/migrate-the-3d-slicer-to-my-own-program/22994)

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**Author:** [@zhiyuan](https://discourse.slicer.org/u/zhiyuan)\
**Replies:** 2\
**Last updated:** [April 18, 2022, 9:06am UTC](https://discourse.slicer.org/t/migrate-the-3d-slicer-to-my-own-program/22994 "2022-04-18T09:06:32Z")

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Can I migrate the 3D slicer view and measurement functions directly to my own Python program? If I can, what information do I need to learn or check

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## [No module named 'xeus\_python\_shell' when installing SlicerJupyter on SlicerCAT](https://discourse.slicer.org/t/no-module-named-xeus-python-shell-when-installing-slicerjupyter-on-slicercat/22985)

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**Author:** [@keri](https://discourse.slicer.org/u/keri)\
**Replies:** 13\
**Last updated:** [April 18, 2022, 1:06am UTC](https://discourse.slicer.org/t/no-module-named-xeus-python-shell-when-installing-slicerjupyter-on-slicercat/22985 "2022-04-18T01:06:20Z")

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Hi, To build SlicerJupyter I use the hints from the link After building SlicerCAT with SlicerJupyter I click on Start Jupyter Server button and after a while the Jupyter runs. After new instances of SlicerCAT are laun…

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## [How to add the Subject hierarchy tree to a custom extension](https://discourse.slicer.org/t/how-to-add-the-subject-hierarchy-tree-to-a-custom-extension/22980)

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**Author:** [@koeglfryderyk](https://discourse.slicer.org/u/koeglfryderyk)\
**Replies:** 2\
**Last updated:** [April 16, 2022, 3:07pm UTC](https://discourse.slicer.org/t/how-to-add-the-subject-hierarchy-tree-to-a-custom-extension/22980 "2022-04-16T15:07:26Z")

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I wanted to have the subject hierarchy as part of my custom extension. To do this, I added the qMRMLSubjectHierarchyTreeView to my .ui file. It now appears in my custom extension but it is empty (a scene is loaded and …

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## [Setting segmentation in SegmentEditor without changing volumes in slice views](https://discourse.slicer.org/t/setting-segmentation-in-segmenteditor-without-changing-volumes-in-slice-views/22977)

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**Author:** [@vanossj](https://discourse.slicer.org/u/vanossj)\
**Replies:** 3\
**Last updated:** [April 16, 2022, 12:59pm UTC](https://discourse.slicer.org/t/setting-segmentation-in-segmenteditor-without-changing-volumes-in-slice-views/22977 "2022-04-16T12:59:49Z")

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I’ve setup 3DSlicer to load different volumes in different slice views, red, green, etc. There are also a separate segmentation node for each of these volumes. These segmentation nodes are displayed only on the slice vie…

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## [Get IJK coordinate](https://discourse.slicer.org/t/get-ijk-coordinate/22650)

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**Author:** [@Haytham](https://discourse.slicer.org/u/Haytham)\
**Replies:** 2\
**Last updated:** [March 28, 2022, 9:27am UTC](https://discourse.slicer.org/t/get-ijk-coordinate/22650 "2022-03-28T09:27:08Z")

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Hello, how we can get the click coordinate of the mouse in IJK coordinate system? we need to select the segmentation voxel, I am trying to find the relationship between the coordinate system. we need the transform matr…

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## [In situ visualization and clusters](https://discourse.slicer.org/t/in-situ-visualization-and-clusters/22937)

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**Author:** [@fbordignon](https://discourse.slicer.org/u/fbordignon)\
**Replies:** 5\
**Last updated:** [April 13, 2022, 9:49pm UTC](https://discourse.slicer.org/t/in-situ-visualization-and-clusters/22937 "2022-04-13T21:49:20Z")

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Hello everyone. 3D Slicer has been great the past 3 years that we customized it to the O&G industry. We did not release GeoSlicer to the market yet, but we’ve achieved great improvement over the traditional workflows on …

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## [Loading nrrd data in python Jupyter notebook script](https://discourse.slicer.org/t/loading-nrrd-data-in-python-jupyter-notebook-script/22637)

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**Author:** [@Hanne1234](https://discourse.slicer.org/u/Hanne1234)\
**Replies:** 7\
**Last updated:** [April 12, 2022, 4:49pm UTC](https://discourse.slicer.org/t/loading-nrrd-data-in-python-jupyter-notebook-script/22637 "2022-04-12T16:49:51Z")

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Hi, I am new working with the PyRadiomics package and I have a very basic question. How to load in the data in the Jupyter Notebook script? I used 3D slicer to perform a segmentation on a PET image and I want to load t…

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## [different built version slicer cannot get dicom.instanceUIDs attribute](https://discourse.slicer.org/t/different-built-version-slicer-cannot-get-dicom-instanceuids-attribute/22599)

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**Author:** [@luxiaoyanglxy9999](https://discourse.slicer.org/u/luxiaoyanglxy9999)\
**Replies:** 9\
**Last updated:** [April 9, 2022, 6:23pm UTC](https://discourse.slicer.org/t/different-built-version-slicer-cannot-get-dicom-instanceuids-attribute/22599 "2022-04-09T18:23:36Z")

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Hi, When use a self-build verison slicer (the latest slicer code and source code version: Slicer-88f0c40fa19d00616ba984abd0512e540a974525), I found I cannot get the DICOM.instanceUIDs vtkMRMLScalarVolumeNode as follows. …

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