# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?no_subcategories=false&page=89

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

**Page:** 90

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## [Build error curl/libssh2](https://discourse.slicer.org/t/build-error-curl-libssh2/12809)

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**Author:** [@gcsharp](https://discourse.slicer.org/u/gcsharp)\
**Replies:** 4\
**Last updated:** [July 31, 2020, 8:27pm UTC](https://discourse.slicer.org/t/build-error-curl-libssh2/12809 "2020-07-31T20:27:02Z")

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Hi, I am getting the following build error: \[ 23%\] Linking CXX shared library ../../bin/libRemoteIO.so /usr/bin/ld: /PHShome/gcs6/build/slicer-4/Slicer-build/curl-install/lib/libcurl.a(libssh2.c.o): in function \`ssh\_sta…

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## [MacOS Catalina 10.15.5 compilation error](https://discourse.slicer.org/t/macos-catalina-10-15-5-compilation-error/12807)

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**Author:** [@che85](https://discourse.slicer.org/u/che85)\
**Replies:** 8\
**Last updated:** [July 31, 2020, 6:44pm UTC](https://discourse.slicer.org/t/macos-catalina-10-15-5-compilation-error/12807 "2020-07-31T18:44:29Z")

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Hi everyone, I am experiencing compilation errors. herzc@54ee75c68e2e ~/D/S4D\> /Library/Developer/CommandLineTools/usr/bin/gcc --version Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-incl…

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## [Slicer crashes when setting master Sequence Node to SequenceBrowserNode](https://discourse.slicer.org/t/slicer-crashes-when-setting-master-sequence-node-to-sequencebrowsernode/12795)

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**Author:** [@dloopz](https://discourse.slicer.org/u/dloopz)\
**Replies:** 2\
**Last updated:** [July 31, 2020, 3:31pm UTC](https://discourse.slicer.org/t/slicer-crashes-when-setting-master-sequence-node-to-sequencebrowsernode/12795 "2020-07-31T15:31:59Z")

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Operating system: Ubuntu Debian 18.04 (KDE neon 5.19) Slicer version: 4.11.0-2020-06-05 Expected behavior: Actual behavior: Hi everyone, I’m having some troubles managing sequences (create them and remove them compl…

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## [Zoom in/out mouse controls and orientation not working in a a slice view outside the view layout](https://discourse.slicer.org/t/zoom-in-out-mouse-controls-and-orientation-not-working-in-a-a-slice-view-outside-the-view-layout/12783)

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**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\
**Replies:** 4\
**Last updated:** [July 31, 2020, 12:55pm UTC](https://discourse.slicer.org/t/zoom-in-out-mouse-controls-and-orientation-not-working-in-a-a-slice-view-outside-the-view-layout/12783 "2020-07-31T12:55:40Z")

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Hi everyone, I follow the scrypt repository example for adding a slice view outside the view layout and it works straightforward but I have some trouble with volumes managing. 1.- Mouse controls (zoom, move, scroll sli…

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## [Detect when slice layer changes](https://discourse.slicer.org/t/detect-when-slice-layer-changes/12775)

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**Author:** [@Jakew](https://discourse.slicer.org/u/Jakew)\
**Replies:** 4\
**Last updated:** [July 31, 2020, 2:58am UTC](https://discourse.slicer.org/t/detect-when-slice-layer-changes/12775 "2020-07-31T02:58:17Z")

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I’m looking for a way to detect when the scroll bar at the top of a view moves, or when the slice view changes. This can be done by detecting when the scroll wheel moves or when arrow keys are used, but I’d like to be ab…

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## [Model opacity change in single view](https://discourse.slicer.org/t/model-opacity-change-in-single-view/4707)

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**Author:** [@priya.vada4](https://discourse.slicer.org/u/priya.vada4)\
**Replies:** 4\
**Last updated:** [July 30, 2020, 10:14pm UTC](https://discourse.slicer.org/t/model-opacity-change-in-single-view/4707 "2020-07-30T22:14:33Z")

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Hi When the Slicer display is setup in the Triple 3D view, is it possible to change the opacity of a model only in 1 view while the model opacity remains the same in the other two views. I know it is possible to change …

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## [Convert voxels to grayscale](https://discourse.slicer.org/t/convert-voxels-to-grayscale/12376)

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**Author:** [@talmazov](https://discourse.slicer.org/u/talmazov)\
**Replies:** 2\
**Last updated:** [July 30, 2020, 9:57pm UTC](https://discourse.slicer.org/t/convert-voxels-to-grayscale/12376 "2020-07-30T21:57:18Z")

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Hey, I am using slicer.util.arrayFromVolume to obtain an array of my slice widget view. However, the array contains voxel data, how can i convert that to RGB grayscale? Thanks

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## [Slicer ROI dimensions Input numbers autofill](https://discourse.slicer.org/t/slicer-roi-dimensions-input-numbers-autofill/12773)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 6\
**Last updated:** [July 30, 2020, 12:04am UTC](https://discourse.slicer.org/t/slicer-roi-dimensions-input-numbers-autofill/12773 "2020-07-30T00:04:17Z")

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Hi, it is bit annoying when we type in the dimensions of ROI box that it autofills the next number. I am not sure if I explain it properly. For example if I want to type 0.75 and the moment I type 0.7 it fills the 0. S…

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## [JupyterNotebooksLib Slicer - functions to edit volume rendering parameters?](https://discourse.slicer.org/t/jupyternotebookslib-slicer-functions-to-edit-volume-rendering-parameters/12776)

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**Author:** [@allihuwa](https://discourse.slicer.org/u/allihuwa)\
**Replies:** 0\
**Last updated:** [July 29, 2020, 9:19pm UTC](https://discourse.slicer.org/t/jupyternotebookslib-slicer-functions-to-edit-volume-rendering-parameters/12776 "2020-07-29T21:19:10Z")

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Hi, I am able to successfully load a volume into the SlicerWeb extension and use the JupyterNotebookLib. What I wanted to do now is use functions in this library that enable me to change the volume rendering presets and …

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## [GetID() and GetName() methods giving different nodes](https://discourse.slicer.org/t/getid-and-getname-methods-giving-different-nodes/12769)

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**Author:** [@dloopz](https://discourse.slicer.org/u/dloopz)\
**Replies:** 1\
**Last updated:** [July 29, 2020, 2:21pm UTC](https://discourse.slicer.org/t/getid-and-getname-methods-giving-different-nodes/12769 "2020-07-29T14:21:20Z")

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Operating system: Ubuntu Debian 18.04 (KDE neon 5.19) Slicer version: 4.11.0-2020-06-05 Expected behavior: Getting unic node by its ID Actual behavior: Getting other node ID by GetID() method Hi! I’m devoloping a se…

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## [Problem in Editor module](https://discourse.slicer.org/t/problem-in-editor-module/12739)

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**Author:** [@fpsiddiqui91](https://discourse.slicer.org/u/fpsiddiqui91)\
**Replies:** 6\
**Last updated:** [July 28, 2020, 10:41pm UTC](https://discourse.slicer.org/t/problem-in-editor-module/12739 "2020-07-28T22:41:37Z")

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I am trying to build Slicer again in my windows machine. I have some problem in loading the editor module. When I am switching to the Editor module, I am getting this error: Traceback (most recent call last): File "C…

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## [Using variables from module1 in module2](https://discourse.slicer.org/t/using-variables-from-module1-in-module2/12752)

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**Author:** [@rohan\_n](https://discourse.slicer.org/u/rohan_n)\
**Replies:** 3\
**Last updated:** [July 28, 2020, 11:09pm UTC](https://discourse.slicer.org/t/using-variables-from-module1-in-module2/12752 "2020-07-28T23:09:14Z")

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I have two modules, module1 and module2. I am asking the user to select a folder using qFileDialog in this part of module 1 class module1Logic(ScriptedLoadableModuleLogic): def run(self): exampath = qt.QFileDialog.get…

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## [Proposed new SlicerAstro logo](https://discourse.slicer.org/t/proposed-new-slicerastro-logo/12601)

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**Author:** [@Davide\_Punzo](https://discourse.slicer.org/u/Davide_Punzo)\
**Replies:** 17\
**Last updated:** [July 28, 2020, 9:35pm UTC](https://discourse.slicer.org/t/proposed-new-slicerastro-logo/12601 "2020-07-28T21:35:52Z")

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Edit (@jcfr): This topic is a follow up of Proposed new Slicer logo - #74 I was playing just for fun a little bit with the new Slicer icon for upting the SlicerAstro one. Here my first experiment (I am super amateur i…

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## [Apply transform to a volume](https://discourse.slicer.org/t/apply-transform-to-a-volume/12594)

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**Author:** [@Stweie](https://discourse.slicer.org/u/Stweie)\
**Replies:** 9\
**Last updated:** [July 28, 2020, 7:30pm UTC](https://discourse.slicer.org/t/apply-transform-to-a-volume/12594 "2020-07-28T19:30:50Z")

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I used python script to use the landmark registration plugin and applied a custom transformation matrix like following: transformed\_node = slicer.util.getNode(“Transform”) transformed\_node.SetMatrixTransformToParent(re…

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## [Set linear transform parameter via python](https://discourse.slicer.org/t/set-linear-transform-parameter-via-python/12742)

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**Author:** [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Replies:** 4\
**Last updated:** [July 28, 2020, 9:39am UTC](https://discourse.slicer.org/t/set-linear-transform-parameter-via-python/12742 "2020-07-28T09:39:21Z")

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Hi all, I would like to set and control a linear transformation from python. I created a linear transformation via the module GUI and then I changed a parameter (just to do a test). If I run this code nothing changes …

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## [Slicer builded version crash at startup, ntdll problem ](https://discourse.slicer.org/t/slicer-builded-version-crash-at-startup-ntdll-problem/12702)

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**Author:** [@Zian\_Fanti](https://discourse.slicer.org/u/Zian_Fanti)\
**Replies:** 8\
**Last updated:** [July 28, 2020, 1:30am UTC](https://discourse.slicer.org/t/slicer-builded-version-crash-at-startup-ntdll-problem/12702 "2020-07-28T01:30:29Z")

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Operating system: Windows 10 Pro Slicer version: 4.11.0 commit 3d72c1f I successfully build slicer using Visual Studio 19. But crashes when I try to run it. I got the following in the log file: \[DEBUG\]\[Qt\] 22.07.2020 …

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## [Proposed changes to Markups to support unplaced points](https://discourse.slicer.org/t/proposed-changes-to-markups-to-support-unplaced-points/12714)

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**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 13\
**Last updated:** [July 27, 2020, 9:44pm UTC](https://discourse.slicer.org/t/proposed-changes-to-markups-to-support-unplaced-points/12714 "2020-07-27T21:44:38Z")

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I’d like to help implement some updates to support the use of unplaced fiducials, as discussed in this thread. From that discussion and our user needs, I made a detailed list of improvements and would appreciate feedback…

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## [Differentiating between 2 vtkMRMLAnnotationROINodes](https://discourse.slicer.org/t/differentiating-between-2-vtkmrmlannotationroinodes/12727)

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**Author:** [@rohan\_n](https://discourse.slicer.org/u/rohan_n)\
**Replies:** 1\
**Last updated:** [July 25, 2020, 12:33am UTC](https://discourse.slicer.org/t/differentiating-between-2-vtkmrmlannotationroinodes/12727 "2020-07-25T00:33:24Z")

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Hello, Let’s say I’ve done the following: a = slicer.vtkMRMLAnnotationROINode() slicer.mrmlScene.AddNode(a) b = slicer.vtkMRMLAnnotationROINode() slicer.mrmlScene.AddNode(b) And the user is looking at an image in t…

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## [How to associate colormap with the model](https://discourse.slicer.org/t/how-to-associate-colormap-with-the-model/12724)

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**Author:** [@siaeleni](https://discourse.slicer.org/u/siaeleni)\
**Replies:** 1\
**Last updated:** [July 24, 2020, 5:51pm UTC](https://discourse.slicer.org/t/how-to-associate-colormap-with-the-model/12724 "2020-07-24T17:51:08Z")

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Hi, I want to add a colormap in 3DView and show the min-max actual values with the same color as my model. I am generating a model and you can see the output at the image attached. I can display a color map, but I h…

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## [ITK image to mesh to vtk polydata](https://discourse.slicer.org/t/itk-image-to-mesh-to-vtk-polydata/12717)

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**Author:** [@Zhiy](https://discourse.slicer.org/u/Zhiy)\
**Replies:** 2\
**Last updated:** [July 24, 2020, 2:59pm UTC](https://discourse.slicer.org/t/itk-image-to-mesh-to-vtk-polydata/12717 "2020-07-24T14:59:49Z")

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Dear all, Recently I am trying to extract the surface geometry from a binary ITK image (resulting from ostu\_threshold\_image\_filter) into ITK mesh. Then convert this ITK MESH to a vtk polydata. The filters I used includ…

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## [Set Color and Opacity to all Visible Models](https://discourse.slicer.org/t/set-color-and-opacity-to-all-visible-models/12699)

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**Author:** [@Ryan\_Morrison](https://discourse.slicer.org/u/Ryan_Morrison)\
**Replies:** 11\
**Last updated:** [July 23, 2020, 6:11pm UTC](https://discourse.slicer.org/t/set-color-and-opacity-to-all-visible-models/12699 "2020-07-23T18:11:26Z")

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I’d like to apply a R,G,B value and opacity to hundreds of models all at once. I would like to apply the color and opacity only to visible models in the 3D view. I’ve created a python extension, but the code is not quite…

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## [Segfault when calling destructor on ctkDICOMIndexer and ctkDICOMDatabase](https://discourse.slicer.org/t/segfault-when-calling-destructor-on-ctkdicomindexer-and-ctkdicomdatabase/12653)

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**Author:** [@Jakew](https://discourse.slicer.org/u/Jakew)\
**Replies:** 1\
**Last updated:** [July 23, 2020, 2:00am UTC](https://discourse.slicer.org/t/segfault-when-calling-destructor-on-ctkdicomindexer-and-ctkdicomdatabase/12653 "2020-07-23T02:00:31Z")

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I am working on a loadable module extension in which I create a new ctkDICOMIndexer object and a new ctkDICOMDatabase, which I delete in the extension’s destructor. However, when I quit my application, a segfault occurs.…

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## [Running a Scripted CLI Module in Parallel](https://discourse.slicer.org/t/running-a-scripted-cli-module-in-parallel/12687)

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**Author:** [@vertebrae](https://discourse.slicer.org/u/vertebrae)\
**Replies:** 0\
**Last updated:** [July 22, 2020, 2:03pm UTC](https://discourse.slicer.org/t/running-a-scripted-cli-module-in-parallel/12687 "2020-07-22T14:03:46Z")

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Hello, I have a local threshold segmentation code in a scripted python module which iterates through fiducial points and runs the local threshold function. Iterating through points takes a while to do and to speed it up…

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## [Subject Hierarchy ExportAs plugin working only for some systems](https://discourse.slicer.org/t/subject-hierarchy-exportas-plugin-working-only-for-some-systems/12696)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [July 22, 2020, 11:30pm UTC](https://discourse.slicer.org/t/subject-hierarchy-exportas-plugin-working-only-for-some-systems/12696 "2020-07-22T23:30:05Z")

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@pieper implemented an ExportAs plugin for SlicerMorph extension which enables Export As a right-click context menu in the Data module. For markup nodes, this works 100% from the Markups module. For other data types (nam…

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## [Creating Output Master Volume](https://discourse.slicer.org/t/creating-output-master-volume/12690)

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**Author:** [@vertebrae](https://discourse.slicer.org/u/vertebrae)\
**Replies:** 2\
**Last updated:** [July 22, 2020, 2:34pm UTC](https://discourse.slicer.org/t/creating-output-master-volume/12690 "2020-07-22T14:34:41Z")

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Hello, When I run my local threshold segmentation code, 3D Slicer automatically creates an output master volume for my code. Instead, I would like to create a new master volume that could be my output volume after the s…

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## [Extract connected components from polydata structures](https://discourse.slicer.org/t/extract-connected-components-from-polydata-structures/12673)

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**Author:** [@loubna](https://discourse.slicer.org/u/loubna)\
**Replies:** 1\
**Last updated:** [July 22, 2020, 2:18pm UTC](https://discourse.slicer.org/t/extract-connected-components-from-polydata-structures/12673 "2020-07-22T14:18:12Z")

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Hi; Is there any way to extract connected components from a set of planar contours (polydata)? As shown in attached figure, I have two structures and I want to extract each of them as one component. I have found this …

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## [Slicer fails on startup in debug mode if temporary folder is set to empty](https://discourse.slicer.org/t/slicer-fails-on-startup-in-debug-mode-if-temporary-folder-is-set-to-empty/12607)

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**Author:** [@sogo](https://discourse.slicer.org/u/sogo)\
**Replies:** 6\
**Last updated:** [July 19, 2020, 5:14am UTC](https://discourse.slicer.org/t/slicer-fails-on-startup-in-debug-mode-if-temporary-folder-is-set-to-empty/12607 "2020-07-19T05:14:17Z")

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I’m working on an loadable application where I’m changing the temporary directory path to work in my own application directory. I’m changing the directory path by using qSlicerCoreApplication::application-\>setTemporaryPa…

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## [Clone Markups Node Issue](https://discourse.slicer.org/t/clone-markups-node-issue/12602)

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**Author:** [@mjg](https://discourse.slicer.org/u/mjg)\
**Replies:** 1\
**Last updated:** [July 17, 2020, 5:37pm UTC](https://discourse.slicer.org/t/clone-markups-node-issue/12602 "2020-07-17T17:37:48Z")

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Hello, I need to clone line, curve, and closed curve nodes. When I use the method in the script repository it creates a trace of the original node. Does anyone have a fix or better method? I am using Python. The leftmo…

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## [How to install ITK python wheels with Slicer 4.10 and Slicer 4.11?](https://discourse.slicer.org/t/how-to-install-itk-python-wheels-with-slicer-4-10-and-slicer-4-11/12537)

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**Author:** [@siaeleni](https://discourse.slicer.org/u/siaeleni)\
**Replies:** 7\
**Last updated:** [July 16, 2020, 3:08am UTC](https://discourse.slicer.org/t/how-to-install-itk-python-wheels-with-slicer-4-10-and-slicer-4-11/12537 "2020-07-16T03:08:05Z")

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Hello, I have two questions related to itk installation: I want to install itk at 4.10 Slicer version but gives me error: Command “python setup.py egg\_info” failed with error code 1 in c:\\users\\siael\\appdata\\local\\te…

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## [Segment ids when imported from label map](https://discourse.slicer.org/t/segment-ids-when-imported-from-label-map/12502)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 3\
**Last updated:** [July 15, 2020, 4:18pm UTC](https://discourse.slicer.org/t/segment-ids-when-imported-from-label-map/12502 "2020-07-15T16:18:22Z")

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I have a label map with numbers which I would like to keep when I convert it to a segment but I don’t know if this is possible. For example i have labels 1,3,5,8 but I think I loose them to segment 0 1 2 and 4. I have …

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