# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?no_subcategories=false&page=97

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

**Page:** 98

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## [Crop Volume Shutdown](https://discourse.slicer.org/t/crop-volume-shutdown/10510)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 3\
**Last updated:** [March 3, 2020, 5:28pm UTC](https://discourse.slicer.org/t/crop-volume-shutdown/10510 "2020-03-03T17:28:03Z")

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I am encountering rather strange behavior of 3D Slicer when it comes to cropping the volumes of .nii files. Most of the files that i am working are 3 GB +. I have recorded a clip of this rather strange behaviour. Lo…

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## [Scaling volume in slice view](https://discourse.slicer.org/t/scaling-volume-in-slice-view/10517)

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**Author:** [@ZiyunLiang](https://discourse.slicer.org/u/ZiyunLiang)\
**Replies:** 1\
**Last updated:** [March 3, 2020, 4:14pm UTC](https://discourse.slicer.org/t/scaling-volume-in-slice-view/10517 "2020-03-03T16:14:07Z")

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Hi developers, I have a problem about scaling an image in slice view. I’m working on dynamic pelvic floor images and trying to get the rest and strain images of the same person to be the same size in slicer. Is there an…

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## [Build errors using slicer 3D](https://discourse.slicer.org/t/build-errors-using-slicer-3d/10522)

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**Author:** [@loubna](https://discourse.slicer.org/u/loubna)\
**Replies:** 1\
**Last updated:** [March 3, 2020, 3:57pm UTC](https://discourse.slicer.org/t/build-errors-using-slicer-3d/10522 "2020-03-03T15:57:58Z")

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Hi, I try the re-implement the VTKMPUReconstruction method using slicer3D. The slicer3D is compiled without errors. I create a new extension , add a module and I tried implement a non -optimezd marching cubes and some o…

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## [Create coordinate system using model node](https://discourse.slicer.org/t/create-coordinate-system-using-model-node/10313)

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**Author:** [@ZiyunLiang](https://discourse.slicer.org/u/ZiyunLiang)\
**Replies:** 12\
**Last updated:** [March 3, 2020, 3:38am UTC](https://discourse.slicer.org/t/create-coordinate-system-using-model-node/10313 "2020-03-03T03:38:01Z")

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Hi, everyone, I’m trying to create a coordinate system which can be shown and transformed in slice view as shown in the picture below. I tried using CreateModels from SlicerIGT, however, there is only one arrow head i…

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## [Problem in Point Orientation](https://discourse.slicer.org/t/problem-in-point-orientation/10506)

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**Author:** [@brhoom](https://discourse.slicer.org/u/brhoom)\
**Replies:** 3\
**Last updated:** [March 3, 2020, 1:34am UTC](https://discourse.slicer.org/t/problem-in-point-orientation/10506 "2020-03-03T01:34:47Z")

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Dear all, I got a dataset from VerSeg challenge. It has json files that describes center points of vertebral bodies in a 3D image. here is what ir says: The centroid annotations are with respect to the coordinate axi…

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## [Cannot attach Python Debugger from Visual Studio 2017](https://discourse.slicer.org/t/cannot-attach-python-debugger-from-visual-studio-2017/10495)

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**Author:** [@rprueckl](https://discourse.slicer.org/u/rprueckl)\
**Replies:** 1\
**Last updated:** [March 2, 2020, 7:17pm UTC](https://discourse.slicer.org/t/cannot-attach-python-debugger-from-visual-studio-2017/10495 "2020-03-02T19:17:04Z")

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Hi, I tried to debug a custom python scripted module using Visual Studio 2017. I use Slicer 4.11.0-2020-02-26 and installed the python debugger module. I followed these steps: Documentation/Nightly/Extensions/Debugging…

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## [Screen Capture module makes Slicer hang](https://discourse.slicer.org/t/screen-capture-module-makes-slicer-hang/10456)

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**Author:** [@Fernando](https://discourse.slicer.org/u/Fernando)\
**Replies:** 4\
**Last updated:** [March 1, 2020, 10:29am UTC](https://discourse.slicer.org/t/screen-capture-module-makes-slicer-hang/10456 "2020-03-01T10:29:48Z")

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Hi all, When I try to make a GIF with the Screen Capture module, Slicer hangs and I need to force quit. I’m quite confident it happens when ffmpeg is called. I open Slicer from zsh and I think this shell is not happy wi…

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## [Path length issue for segment editor extra effects](https://discourse.slicer.org/t/path-length-issue-for-segment-editor-extra-effects/10481)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 2\
**Last updated:** [March 1, 2020, 2:20am UTC](https://discourse.slicer.org/t/path-length-issue-for-segment-editor-extra-effects/10481 "2020-03-01T02:20:19Z")

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I’m passing on an issue that @muratmaga experienced at a recent training event, where one of the users found that SegmentEditorExtraEffects would not load unless moved to a shorter path: Path issues are also very big c…

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## [Simple menu in scene](https://discourse.slicer.org/t/simple-menu-in-scene/10484)

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**Author:** [@FloridaMan](https://discourse.slicer.org/u/FloridaMan)\
**Replies:** 1\
**Last updated:** [March 1, 2020, 1:18am UTC](https://discourse.slicer.org/t/simple-menu-in-scene/10484 "2020-03-01T01:18:50Z")

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I am looking to put a vtk menu in the scene where the volume is and have it locked to the camera. Does anyone have advice on what will need to be setup for this? Currently trying to follow reformat modules as an example. …

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## [Connecting two or more volumes](https://discourse.slicer.org/t/connecting-two-or-more-volumes/9922)

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**Author:** [@tkt8](https://discourse.slicer.org/u/tkt8)\
**Replies:** 7\
**Last updated:** [February 28, 2020, 4:38pm UTC](https://discourse.slicer.org/t/connecting-two-or-more-volumes/9922 "2020-02-28T16:38:01Z")

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I am developing an extension for slicer. I wanted to compare the original volume and the modified volume. Is there a way to link the two so that I can mimic the action such as say segmentation done in original volume is …

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## [New \`highdicom\` python library](https://discourse.slicer.org/t/new-highdicom-python-library/10468)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 0\
**Last updated:** [February 28, 2020, 3:09pm UTC](https://discourse.slicer.org/t/new-highdicom-python-library/10468 "2020-02-28T15:09:58Z")

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Good news for dicom developers: a new python library for has just been made public under the MIT license for multiframes, segmentation, reporting, and related topics. It can be pip\_installed into the Slicer nightly if y…

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## [Machine Learning Model Importing](https://discourse.slicer.org/t/machine-learning-model-importing/6298)

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**Author:** [@coolsocks](https://discourse.slicer.org/u/coolsocks)\
**Replies:** 9\
**Last updated:** [February 27, 2020, 1:52pm UTC](https://discourse.slicer.org/t/machine-learning-model-importing/6298 "2020-02-27T13:52:25Z")

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Hi! I am currently building a module which involves importing a deep learning model trained with keras to predict some segmentations. Initially, the question I had was how to go about running the keras/tensorflow packag…

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## [Easy Clip Extension - Not loading in Linux](https://discourse.slicer.org/t/easy-clip-extension-not-loading-in-linux/10430)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 1\
**Last updated:** [February 25, 2020, 6:59pm UTC](https://discourse.slicer.org/t/easy-clip-extension-not-loading-in-linux/10430 "2020-02-25T18:59:19Z")

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The easy clip extension and several other extensions like angleplanes,q3dc are failing to load in my machine. It woks in the stable release. This has been the case for several previous preview release which i noticed. …

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## [Getting vtkMRMLSliceNodeGreen, vtkMRMLSliceNodeRed, vtkMRMLSliceNodeYellow data into numpy array](https://discourse.slicer.org/t/getting-vtkmrmlslicenodegreen-vtkmrmlslicenodered-vtkmrmlslicenodeyellow-data-into-numpy-array/10422)

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**Author:** [@dataminer](https://discourse.slicer.org/u/dataminer)\
**Replies:** 3\
**Last updated:** [February 25, 2020, 6:40pm UTC](https://discourse.slicer.org/t/getting-vtkmrmlslicenodegreen-vtkmrmlslicenodered-vtkmrmlslicenodeyellow-data-into-numpy-array/10422 "2020-02-25T18:40:36Z")

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Hello Everyone I am new to slicer. I can import NRRD file and see the 3 views (sagittal, coronal and transverse), and I can use 3DSlicer to save them as png file for each of the 3 views (by using ScreenCapture.ScreenCa…

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## [UI state management in scripted modules](https://discourse.slicer.org/t/ui-state-management-in-scripted-modules/10417)

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**Author:** [@James\_Hoctor](https://discourse.slicer.org/u/James_Hoctor)\
**Replies:** 2\
**Last updated:** [February 25, 2020, 5:13am UTC](https://discourse.slicer.org/t/ui-state-management-in-scripted-modules/10417 "2020-02-25T05:13:43Z")

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I need design guidance for choosing where to keep canonical UI state in a scripted Slicer module. The module in question is PickAndPaint. The complicated design of the data structures in this module seems to be the root …

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## [Install Python packages with extension manager](https://discourse.slicer.org/t/install-python-packages-with-extension-manager/10419)

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**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 2\
**Last updated:** [February 24, 2020, 10:29pm UTC](https://discourse.slicer.org/t/install-python-packages-with-extension-manager/10419 "2020-02-24T22:29:52Z")

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Now that slicer.util.pip\_install has streamlined the installation of python packages, I’d like to revisit the conversation on automated installation of python packages. We’d like to have users install a few python packa…

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## [General Registration(Elastix) problem!](https://discourse.slicer.org/t/general-registration-elastix-problem/10281)

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**Author:** [@endlessric23](https://discourse.slicer.org/u/endlessric23)\
**Replies:** 5\
**Last updated:** [February 23, 2020, 3:42pm UTC](https://discourse.slicer.org/t/general-registration-elastix-problem/10281 "2020-02-23T15:42:11Z")

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Dear Slicer user I am using the General Registration(Elastix) tool,when I use the parameter (Preset)“2D x-ray - 3D CT(cerebral)”,there’s some error occured. The detailed log is in the following line.Seems like the libr…

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## [Linux revision 28779 - Segment editor](https://discourse.slicer.org/t/linux-revision-28779-segment-editor/10398)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 4\
**Last updated:** [February 23, 2020, 8:27am UTC](https://discourse.slicer.org/t/linux-revision-28779-segment-editor/10398 "2020-02-23T08:27:52Z")

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When i try use Island effects, Slicer exist with the following error message, error: \[/\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/Slicer-4.11.0-2020-02-19-linux-amd64/bin/SlicerApp-real\] exit abnormally - Report the problem. This happens with l…

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## [Fill a newly created parameter node](https://discourse.slicer.org/t/fill-a-newly-created-parameter-node/10391)

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**Author:** [@Juicy](https://discourse.slicer.org/u/Juicy)\
**Replies:** 2\
**Last updated:** [February 22, 2020, 10:16am UTC](https://discourse.slicer.org/t/fill-a-newly-created-parameter-node/10391 "2020-02-22T10:16:23Z")

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I have some confusion regarding the creation of a new parameter node for a scripted module. I have seen in other modules that you can over-ride the base class createParameterNode method in the logic class so that you ca…

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## [Can I select the modleNode with mouse?](https://discourse.slicer.org/t/can-i-select-the-modlenode-with-mouse/10285)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 1\
**Last updated:** [February 20, 2020, 8:02am UTC](https://discourse.slicer.org/t/can-i-select-the-modlenode-with-mouse/10285 "2020-02-20T08:02:31Z")

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The slicer can select the markupFiducials with mouse but I donnot know can I use the mouse select the modelNode?

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## [Get LabelMap voxel values](https://discourse.slicer.org/t/get-labelmap-voxel-values/10337)

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**Author:** [@loubna](https://discourse.slicer.org/u/loubna)\
**Replies:** 12\
**Last updated:** [February 20, 2020, 3:55am UTC](https://discourse.slicer.org/t/get-labelmap-voxel-values/10337 "2020-02-20T03:55:51Z")

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how can we extract points from binary volume (labelMap). I confuse between the vertices of each voxel and points. So I need extract points from labelMap. Thank’s in advance

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## [Contour target area for MLC leaf positioning calculation](https://discourse.slicer.org/t/contour-target-area-for-mlc-leaf-positioning-calculation/10101)

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**Author:** [@Mik](https://discourse.slicer.org/u/Mik)\
**Replies:** 1\
**Last updated:** [February 19, 2020, 8:56am UTC](https://discourse.slicer.org/t/contour-target-area-for-mlc-leaf-positioning-calculation/10101 "2020-02-19T08:56:55Z")

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Operating system: linux Slicer version: Preview There are 2 points which define a normal vector 0N (yellow) of the plane (green) for DICOM CT and RTSTRUCT contour data. I can calculate a perpendicular projection of eac…

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## [Rt dose in Sagittal and Coronal plane](https://discourse.slicer.org/t/rt-dose-in-sagittal-and-coronal-plane/10343)

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**Author:** [@Juliana\_Campos\_de\_Fr](https://discourse.slicer.org/u/Juliana_Campos_de_Fr)\
**Replies:** 1\
**Last updated:** [February 18, 2020, 9:18pm UTC](https://discourse.slicer.org/t/rt-dose-in-sagittal-and-coronal-plane/10343 "2020-02-18T21:18:55Z")

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Hello everyone, I am trying to overlay rt dose and rt structure from axial plane into sagittal and coronal plane images in python. I did not find how it is done in slicer rt, can anyone help me to find/undestand how it …

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## [Instantiated AnnotationROI node positioning](https://discourse.slicer.org/t/instantiated-annotationroi-node-positioning/10340)

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**Author:** [@adelmo](https://discourse.slicer.org/u/adelmo)\
**Replies:** 1\
**Last updated:** [February 18, 2020, 5:44pm UTC](https://discourse.slicer.org/t/instantiated-annotationroi-node-positioning/10340 "2020-02-18T17:44:07Z")

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Hello, I would like to instantiate, via Python code, an AnnotationROI node and I would like to automatically position the generated bounding box to enclose exactly a volume node. I am sure it is a super simple operatio…

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## [Data module filter behavior](https://discourse.slicer.org/t/data-module-filter-behavior/10314)

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**Author:** [@giovform](https://discourse.slicer.org/u/giovform)\
**Replies:** 1\
**Last updated:** [February 18, 2020, 2:42pm UTC](https://discourse.slicer.org/t/data-module-filter-behavior/10314 "2020-02-18T14:42:17Z")

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Hi, I have a directory structure within the data module, and I noticed if I write in the filter box a string that doesn’t match any names, it collapses all the directories, and I have to open them all again. If there is …

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## [\[Image Integration\] Ensite Velocity EPS map + CT scan for radiosurgery in patients with VT](https://discourse.slicer.org/t/image-integration-ensite-velocity-eps-map-ct-scan-for-radiosurgery-in-patients-with-vt/10299)

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**Author:** [@tomasz](https://discourse.slicer.org/u/tomasz)\
**Replies:** 1\
**Last updated:** [February 18, 2020, 1:13am UTC](https://discourse.slicer.org/t/image-integration-ensite-velocity-eps-map-ct-scan-for-radiosurgery-in-patients-with-vt/10299 "2020-02-18T01:13:55Z")

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Dear All, My name is Tomasz Jadczyk. I am an assistant professor and EP fellow at the Medical University of Silesia (Department of Cardiology and Structural Heart Diseases). I am interested in the application of 3D Sli…

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## [Simple solution for MRI navigation](https://discourse.slicer.org/t/simple-solution-for-mri-navigation/10316)

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**Author:** [@qeee](https://discourse.slicer.org/u/qeee)\
**Replies:** 1\
**Last updated:** [February 17, 2020, 6:58pm UTC](https://discourse.slicer.org/t/simple-solution-for-mri-navigation/10316 "2020-02-17T18:58:10Z")

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hi guys, I am looking for a simple solution for MRI navigation, I need a pointer which shows location on MRI for example if I point on patella it shows me MRI transverse slice of patella, is it so difficult and do I need…

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## [Linux Preview Release Download Points to old built - FYI](https://discourse.slicer.org/t/linux-preview-release-download-points-to-old-built-fyi/10308)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 1\
**Last updated:** [February 17, 2020, 12:48pm UTC](https://discourse.slicer.org/t/linux-preview-release-download-points-to-old-built-fyi/10308 "2020-02-17T12:48:00Z")

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I expected to download the Linux version of version 4.11.0 revision 28770 built 2020-02-16 However the downloaded version is. Slicer-4.11.0-2020-02-12-linux-amd64

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## [Extract point cloud from labelMap contour](https://discourse.slicer.org/t/extract-point-cloud-from-labelmap-contour/10139)

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**Author:** [@loubna](https://discourse.slicer.org/u/loubna)\
**Replies:** 10\
**Last updated:** [February 16, 2020, 2:19pm UTC](https://discourse.slicer.org/t/extract-point-cloud-from-labelmap-contour/10139 "2020-02-16T14:19:03Z")

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Hi, I want to Apply two filters on a binary volume (labelMap). The first one is 3D Gaussian filter to blur the boundry between inside and outside voxels , and the second one is the sobel filter at the voxel locations co…

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## [How to close the Widget](https://discourse.slicer.org/t/how-to-close-the-widget/10272)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 3\
**Last updated:** [February 16, 2020, 4:45am UTC](https://discourse.slicer.org/t/how-to-close-the-widget/10272 "2020-02-16T04:45:37Z")

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I called the endoscopy with python script such as: import Endoscopy endo=Endoscopy.EndoscopyWidget() But I cannot close it. endo.close() and I get some erro: Traceback (most recent call last): File “”, line 1,…

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