# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?no_subcategories=false&page=48

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

**Page:** 49

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## [Remove Annotations module](https://discourse.slicer.org/t/remove-annotations-module/25271)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 0\
**Last updated:** [September 14, 2022, 4:52pm UTC](https://discourse.slicer.org/t/remove-annotations-module/25271 "2022-09-14T16:52:24Z")

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Annotations module, which provides vtkMRMLAnnotationROI and vtkMRMLAnnotationRuler nodes have been deprecated since April 2021 and will be removed in Slicer-5.4 stable release (around early 2023). all annotation nodes w…

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## [How to find the 2 closest concave points of a concave polygon?](https://discourse.slicer.org/t/how-to-find-the-2-closest-concave-points-of-a-concave-polygon/25258)

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**Author:** [@jumbojing](https://discourse.slicer.org/u/jumbojing)\
**Replies:** 1\
**Last updated:** [September 14, 2022, 3:23pm UTC](https://discourse.slicer.org/t/how-to-find-the-2-closest-concave-points-of-a-concave-polygon/25258 "2022-09-14T15:23:09Z")

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How to find the 2 closest concave points of the :point\_up\_2:t2: concave polygon? pointsArr = np.array(\[\[ 1.9271976e+00, 5.5460022e+01, -1.0658541e+03\], \[ 1.7924013e+00, 5.5538818e+01, -1.0669388e+03\], \[ 2.1858673…

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## [Command response openigtlink](https://discourse.slicer.org/t/command-response-openigtlink/25266)

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**Author:** [@Srijeet\_Chatterjee](https://discourse.slicer.org/u/Srijeet_Chatterjee)\
**Replies:** 0\
**Last updated:** [September 14, 2022, 2:40pm UTC](https://discourse.slicer.org/t/command-response-openigtlink/25266 "2022-09-14T14:40:10Z")

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Hello everyone, My question is, how can I print a received a command message in the igtlinkremote or python interactor? I am sending a command from slicer using: cn=slicer.mrmlScene.GetNodeByID("vtkMRMLIGTLConnect…

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## [How to edit DICOM module](https://discourse.slicer.org/t/how-to-edit-dicom-module/25208)

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**Author:** [@miniminic](https://discourse.slicer.org/u/miniminic)\
**Replies:** 2\
**Last updated:** [September 13, 2022, 12:33pm UTC](https://discourse.slicer.org/t/how-to-edit-dicom-module/25208 "2022-09-13T12:33:09Z")

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I want to modify some of the code and UI of the DICOM module, but when I click Edit, a py.exe appears and then disappears. When I click Edit UI, error: Application does NOT exists \[E:/Company/SlicerBuild/Slicer-build/…

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## [Transform Process question](https://discourse.slicer.org/t/transform-process-question/25193)

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**Author:** [@JBeninca](https://discourse.slicer.org/u/JBeninca)\
**Replies:** 2\
**Last updated:** [September 11, 2022, 12:14pm UTC](https://discourse.slicer.org/t/transform-process-question/25193 "2022-09-11T12:14:53Z")

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Hi, i’ve got a problem with the IGT Transform Process module. it seems does not accept vtkMRMLTransformNode s. and the GUI does not show them. and the cursor to sellect cut-off frequency does not appear has anyone had…

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## [2d segmentation in 3d slicer ](https://discourse.slicer.org/t/2d-segmentation-in-3d-slicer/25164)

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**Author:** [@luna1](https://discourse.slicer.org/u/luna1)\
**Replies:** 6\
**Last updated:** [September 11, 2022, 7:25am UTC](https://discourse.slicer.org/t/2d-segmentation-in-3d-slicer/25164 "2022-09-11T07:25:54Z")

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hello,am trying to programme an extension in python that does brain tumour segmentation. my plan was that i draw a contour around the tumour once in each one of the axes then iterate in each of the slices where the init…

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## [Scissors segment editor effects from a script](https://discourse.slicer.org/t/scissors-segment-editor-effects-from-a-script/8348)

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**Author:** [@giovform](https://discourse.slicer.org/u/giovform)\
**Replies:** 20\
**Last updated:** [September 9, 2022, 3:02am UTC](https://discourse.slicer.org/t/scissors-segment-editor-effects-from-a-script/8348 "2022-09-09T03:02:57Z")

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Hello, I am using this script example and its already working fine for the threshold step I needed to segment my data. I need also to apply the Scissors circle effect, from the axial view, using the following options: o…

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## [Enable automatic extension update check?](https://discourse.slicer.org/t/enable-automatic-extension-update-check/25062)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 6\
**Last updated:** [September 8, 2022, 6:32pm UTC](https://discourse.slicer.org/t/enable-automatic-extension-update-check/25062 "2022-09-08T18:32:22Z")

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Automatic extension update check works really well in Slicer-5.0.3, but since it is not enabled by default and the settings is quite hidden in the extensions manager (see the image below) probably many users are not awar…

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## [Slicer Python Interpreter - Virtual Environment](https://discourse.slicer.org/t/slicer-python-interpreter-virtual-environment/25161)

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**Author:** [@arturpol94](https://discourse.slicer.org/u/arturpol94)\
**Replies:** 1\
**Last updated:** [September 8, 2022, 4:33pm UTC](https://discourse.slicer.org/t/slicer-python-interpreter-virtual-environment/25161 "2022-09-08T16:33:13Z")

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Hi, Is it possible to set the slicer python interpreter so that it compiles in a virtual environment? Thanks Artur

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## [Where to refer for common development setup, tools used (static code analysis, tests, debuggers, etc.), coding conventions and guidelines?](https://discourse.slicer.org/t/where-to-refer-for-common-development-setup-tools-used-static-code-analysis-tests-debuggers-etc-coding-conventions-and-guidelines/25156)

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**Author:** [@mukul](https://discourse.slicer.org/u/mukul)\
**Replies:** 1\
**Last updated:** [September 8, 2022, 1:30pm UTC](https://discourse.slicer.org/t/where-to-refer-for-common-development-setup-tools-used-static-code-analysis-tests-debuggers-etc-coding-conventions-and-guidelines/25156 "2022-09-08T13:30:37Z")

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Hi! Being new to the slicer community, I was thinking of going through the common development setup along with the specific tools used to check the code quality and also adhere to the coding conventions currently being …

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## [Is it possible to make the 3d black area transparent in code?](https://discourse.slicer.org/t/is-it-possible-to-make-the-3d-black-area-transparent-in-code/25140)

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**Author:** [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Replies:** 2\
**Last updated:** [September 8, 2022, 1:39am UTC](https://discourse.slicer.org/t/is-it-possible-to-make-the-3d-black-area-transparent-in-code/25140 "2022-09-08T01:39:52Z")

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## [Segmentation fault occured when qSlicerMainWindow's destructor called](https://discourse.slicer.org/t/segmentation-fault-occured-when-qslicermainwindows-destructor-called/25136)

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**Author:** [@nnzzll](https://discourse.slicer.org/u/nnzzll)\
**Replies:** 0\
**Last updated:** [September 7, 2022, 6:33am UTC](https://discourse.slicer.org/t/segmentation-fault-occured-when-qslicermainwindows-destructor-called/25136 "2022-09-07T06:33:46Z")

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I’m developing a custom application of Slicer. When the program exits, a Segmentation fault occured during calling the destructor of qSlicerMainWindow Here is the call traceback by gdb: #0 0x00007fffedaa1f01 in std::…

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## [Grid projection to make uniform landmarks](https://discourse.slicer.org/t/grid-projection-to-make-uniform-landmarks/25048)

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**Author:** [@joanne40226](https://discourse.slicer.org/u/joanne40226)\
**Replies:** 12\
**Last updated:** [September 7, 2022, 5:44am UTC](https://discourse.slicer.org/t/grid-projection-to-make-uniform-landmarks/25048 "2022-09-07T05:44:50Z")

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Hi community, now i want to generate landmarks uniformly from a grid plane to my volume mesh as the diagram shown below (since i want to generate a mean model of a series of data sets, i need to generate landmarks unifo…

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## [IsPointInROI and GetPlanes not available](https://discourse.slicer.org/t/ispointinroi-and-getplanes-not-available/25054)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 6\
**Last updated:** [September 6, 2022, 8:41pm UTC](https://discourse.slicer.org/t/ispointinroi-and-getplanes-not-available/25054 "2022-09-06T20:41:57Z")

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Hello Slicer users, In my Python script I try to check if a voxel is inside a ROI. I searched the forum and found two options which are: IsPointInROI() and GetPlanes() on the vtkMRMLMarkupsROINode. But on both I get an…

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## [Segments Table Extendend Selection having issue](https://discourse.slicer.org/t/segments-table-extendend-selection-having-issue/25119)

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**Author:** [@ssv](https://discourse.slicer.org/u/ssv)\
**Replies:** 0\
**Last updated:** [September 6, 2022, 11:24am UTC](https://discourse.slicer.org/t/segments-table-extendend-selection-having-issue/25119 "2022-09-06T11:24:28Z")

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Slicer Version : 5.1.0 OS : Windows 11 I am trying to do extended selection mode on segments table the selection works from top to bottom . But when i select bottom to top its only select one row getModuleWidget('Seg…

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## [Problem when getting the vtkImageData of a reformatted slice shown in Red widget](https://discourse.slicer.org/t/problem-when-getting-the-vtkimagedata-of-a-reformatted-slice-shown-in-red-widget/25096)

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**Author:** [@Nguyen\_My](https://discourse.slicer.org/u/Nguyen_My)\
**Replies:** 2\
**Last updated:** [September 6, 2022, 5:51am UTC](https://discourse.slicer.org/t/problem-when-getting-the-vtkimagedata-of-a-reformatted-slice-shown-in-red-widget/25096 "2022-09-06T05:51:40Z")

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SUMMARY Operating system: Windows 10 Slicer version: 5.0.2 Expected behavior: getting the vtkImageData of a reformatted slice shown in Red widget. Actual behavior: the returned vtkImageData is of another volume in the …

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## [I created an extension, but it doesn't have any Slicer UI files in it](https://discourse.slicer.org/t/i-created-an-extension-but-it-doesnt-have-any-slicer-ui-files-in-it/25113)

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**Author:** [@miniminic](https://discourse.slicer.org/u/miniminic)\
**Replies:** 1\
**Last updated:** [September 6, 2022, 2:57am UTC](https://discourse.slicer.org/t/i-created-an-extension-but-it-doesnt-have-any-slicer-ui-files-in-it/25113 "2022-09-06T02:57:17Z")

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I created an extension, but it doesn’t have any Slicer UI files in it

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## [Scalars not calculated when creating new volume](https://discourse.slicer.org/t/scalars-not-calculated-when-creating-new-volume/25102)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 0\
**Last updated:** [September 5, 2022, 1:55pm UTC](https://discourse.slicer.org/t/scalars-not-calculated-when-creating-new-volume/25102 "2022-09-05T13:55:58Z")

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I am recently using Slicer 5.0.3 r30893 / 7ea0f43 and I noticed a strange behaviour when it comes to the scalar range that i get back after filling the vtkImageData. I have a python module that reads scalar values from …

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## [Howto find the largest empty circle amid a set of points, and in an enclosing polygon?](https://discourse.slicer.org/t/howto-find-the-largest-empty-circle-amid-a-set-of-points-and-in-an-enclosing-polygon/25064)

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**Author:** [@jumbojing](https://discourse.slicer.org/u/jumbojing)\
**Replies:** 2\
**Last updated:** [September 3, 2022, 12:59pm UTC](https://discourse.slicer.org/t/howto-find-the-largest-empty-circle-amid-a-set-of-points-and-in-an-enclosing-polygon/25064 "2022-09-03T12:59:53Z")

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Howto find the largest empty circle or Maximum Inscribed Circle amid a set of points, and in an enclosing polygon by python code?

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## [qMRMLSubjectHierarchyTreeView Makes a column uneditable](https://discourse.slicer.org/t/qmrmlsubjecthierarchytreeview-makes-a-column-uneditable/25038)

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**Author:** [@miniminic](https://discourse.slicer.org/u/miniminic)\
**Replies:** 3\
**Last updated:** [September 3, 2022, 12:30pm UTC](https://discourse.slicer.org/t/qmrmlsubjecthierarchytreeview-makes-a-column-uneditable/25038 "2022-09-03T12:30:06Z")

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I created an extension, I want to make nameColumn uneditable, how should i do

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## [I try to replace \`markups\` with \`model\` in \`MarkupsToModel\` , but](https://discourse.slicer.org/t/i-try-to-replace-markups-with-model-in-markupstomodel-but/25018)

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**Author:** [@jumbojing](https://discourse.slicer.org/u/jumbojing)\
**Replies:** 6\
**Last updated:** [September 3, 2022, 12:23pm UTC](https://discourse.slicer.org/t/i-try-to-replace-markups-with-model-in-markupstomodel-but/25018 "2022-09-03T12:23:48Z")

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I try to replace markups with model in MarkupsToModel , but…:point\_down:, what’s wrong? def fids2Mod(fids, curve=True): # if isinstance(fids,str): fids = slicer.util.getNode(fids) outputModel = slicer.mrmlS…

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## [qMRMLSubjectHierarchyTreeView vs2022 error LNK2019](https://discourse.slicer.org/t/qmrmlsubjecthierarchytreeview-vs2022-error-lnk2019/25021)

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**Author:** [@miniminic](https://discourse.slicer.org/u/miniminic)\
**Replies:** 1\
**Last updated:** [August 31, 2022, 6:56am UTC](https://discourse.slicer.org/t/qmrmlsubjecthierarchytreeview-vs2022-error-lnk2019/25021 "2022-08-31T06:56:02Z")

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I added a header file, but I still can’t use qMRMLSubjectHierarchyTreeView,is where I set the wrong

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## [How to replace markups with np.array in application MarkupsToModel](https://discourse.slicer.org/t/how-to-replace-markups-with-np-array-in-application-markupstomodel/25000)

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**Author:** [@jumbojing](https://discourse.slicer.org/u/jumbojing)\
**Replies:** 11\
**Last updated:** [September 3, 2022, 3:21am UTC](https://discourse.slicer.org/t/how-to-replace-markups-with-np-array-in-application-markupstomodel/25000 "2022-09-03T03:21:47Z")

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I want to convert a set of point clouds (np.array) to closed surfaces, How to use np.array directly in MarkupsToModel instead of converting np.array to Markups?

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## [How to make modification of Home module work in Custom Application?](https://discourse.slicer.org/t/how-to-make-modification-of-home-module-work-in-custom-application/24969)

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**Author:** [@nnzzll](https://discourse.slicer.org/u/nnzzll)\
**Replies:** 2\
**Last updated:** [September 2, 2022, 2:24pm UTC](https://discourse.slicer.org/t/how-to-make-modification-of-home-module-work-in-custom-application/24969 "2022-09-02T14:24:34Z")

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I’m developing a custom application of Slicer and successfully build the project. The application is switched to the “Home” module by default and I’d like to make some modification in the “Home” module. However, whatev…

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## [Extension review request : should it be made widely available?](https://discourse.slicer.org/t/extension-review-request-should-it-be-made-widely-available/23941)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 8\
**Last updated:** [September 2, 2022, 1:37pm UTC](https://discourse.slicer.org/t/extension-review-request-should-it-be-made-widely-available/23941 "2022-09-02T13:37:42Z")

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Hi, I tinkered these custom markups that draw primitive shapes, and intend to add a few more shapes. Apart from this practical use, I don’t find any useful application yet, at least in the surgical field of my concern. …

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## [Adding Observer within c++ loadable crashes Slicer](https://discourse.slicer.org/t/adding-observer-within-c-loadable-crashes-slicer/25044)

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**Author:** [@leo](https://discourse.slicer.org/u/leo)\
**Replies:** 0\
**Last updated:** [September 1, 2022, 4:25pm UTC](https://discourse.slicer.org/t/adding-observer-within-c-loadable-crashes-slicer/25044 "2022-09-01T16:25:01Z")

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Hello all! So I was trying to implement this line of code from Python in c++: id = crosshairNode.AddObserver(slicer.vtkMRMLCrosshairNode.CursorPositionModifiedEvent, onMouseMoved) and my first guess was this one: v…

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## [How to use qMRMLSubjectHierarchyTreeView](https://discourse.slicer.org/t/how-to-use-qmrmlsubjecthierarchytreeview/16632)

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**Author:** [@kejuhn](https://discourse.slicer.org/u/kejuhn)\
**Replies:** 1\
**Last updated:** [March 19, 2021, 9:33am UTC](https://discourse.slicer.org/t/how-to-use-qmrmlsubjecthierarchytreeview/16632 "2021-03-19T09:33:28Z")

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I create an extension, and add a loadable module “PluginA”. In default UI, I add a qMRMLSubjectHierarchyTreeView by Qt Designer. After build extension in Visual Studio, several errors occurred. ‘qMRMLSubjectHierarchyT…

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## [Fiducial registration wizard - rigid transform algorithm](https://discourse.slicer.org/t/fiducial-registration-wizard-rigid-transform-algorithm/24976)

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**Author:** [@joanne40226](https://discourse.slicer.org/u/joanne40226)\
**Replies:** 2\
**Last updated:** [August 31, 2022, 3:54am UTC](https://discourse.slicer.org/t/fiducial-registration-wizard-rigid-transform-algorithm/24976 "2022-08-31T03:54:24Z")

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Hi community, i am now wondering about the rigid transform in IGT - Fiducial registration wizard. I want to know about the algorithm or the minimal objective function of the rigid transform for landmarks. However, it d…

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## [How do you integrate custom extensions into Slicer's project](https://discourse.slicer.org/t/how-do-you-integrate-custom-extensions-into-slicers-project/24989)

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**Author:** [@miniminic](https://discourse.slicer.org/u/miniminic)\
**Replies:** 2\
**Last updated:** [August 31, 2022, 3:54am UTC](https://discourse.slicer.org/t/how-do-you-integrate-custom-extensions-into-slicers-project/24989 "2022-08-31T03:54:12Z")

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I created an extension and now I want to integrate it into Slicer’s project, like this.

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## [When I add ui , cxx, h to my module, how can add source file?](https://discourse.slicer.org/t/when-i-add-ui-cxx-h-to-my-module-how-can-add-source-file/20660)

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**Author:** [@kookoo9999](https://discourse.slicer.org/u/kookoo9999)\
**Replies:** 6\
**Last updated:** [August 31, 2022, 3:51am UTC](https://discourse.slicer.org/t/when-i-add-ui-cxx-h-to-my-module-how-can-add-source-file/20660 "2022-08-31T03:51:11Z")

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Hello all. Is there a way to add these(.ui , .cxx , .h ) at once? Do you usually add .cxx and .h after adding ui by one click or easily way?? and I don’t know the roles of a and the rest of the project.(mymodule, my…

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