# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?page=116

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

**Page:** 117

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## [Transform Matrix calculated by GetMatrixTransformBetweenNodes](https://discourse.slicer.org/t/transform-matrix-calculated-by-getmatrixtransformbetweennodes/4069)

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**Author:** [@xxzhou](https://discourse.slicer.org/u/xxzhou)\
**Replies:** 5\
**Last updated:** [September 11, 2018, 6:56pm UTC](https://discourse.slicer.org/t/transform-matrix-calculated-by-getmatrixtransformbetweennodes/4069 "2018-09-11T18:56:23Z")

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Hi! I am new for 3D Slicer, and when I want to use GetMatrixTransformBetweenNodes to calculate transform matrix from source to target, I found that the input “source”&“target” are both vtkMRMLTransformNode. However, I …

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## [Transformation graph for quick calculation of concatenated transforms](https://discourse.slicer.org/t/transformation-graph-for-quick-calculation-of-concatenated-transforms/326)

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**Author:** [@mangotee](https://discourse.slicer.org/u/mangotee)\
**Replies:** 12\
**Last updated:** [September 11, 2018, 5:55pm UTC](https://discourse.slicer.org/t/transformation-graph-for-quick-calculation-of-concatenated-transforms/326 "2018-09-11T17:55:17Z")

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Hi, I am looking for a quick way to compute an in-between transformation between two volume nodes that are not directly connected in a transformation graph. Here is a figure of what I mean: Assume I have several MRI…

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## [Using Slicer plot view signal](https://discourse.slicer.org/t/using-slicer-plot-view-signal/4025)

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**Author:** [@Mateo\_Lopez](https://discourse.slicer.org/u/Mateo_Lopez)\
**Replies:** 7\
**Last updated:** [September 11, 2018, 4:27pm UTC](https://discourse.slicer.org/t/using-slicer-plot-view-signal/4025 "2018-09-11T16:27:28Z")

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Hello, I am not used to coding python scripts for Slicer and I am wondering how I can use the dataSelected signal provided by PlotViews. I am creating some plots to visualize PCA data and I would like to detect when a …

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## [Improving usage of when to use Stable vs Nightly release](https://discourse.slicer.org/t/improving-usage-of-when-to-use-stable-vs-nightly-release/4049)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 5\
**Last updated:** [September 10, 2018, 9:21pm UTC](https://discourse.slicer.org/t/improving-usage-of-when-to-use-stable-vs-nightly-release/4049 "2018-09-10T21:21:05Z")

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Background info Out of a discussion that started here I’m thinking there might be some improvement to encourage users when it is best to use the Stable versus the current Nightly release. I frequently see users on the fo…

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## [Internal compiler error in SimpleITK while building Slicer with latest VS2015 compiler](https://discourse.slicer.org/t/internal-compiler-error-in-simpleitk-while-building-slicer-with-latest-vs2015-compiler/4053)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 1\
**Last updated:** [September 10, 2018, 8:03pm UTC](https://discourse.slicer.org/t/internal-compiler-error-in-simpleitk-while-building-slicer-with-latest-vs2015-compiler/4053 "2018-09-10T20:03:31Z")

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I’ve recently updated my VS2015 compiler (used in VS2017 IDE) to “Microsoft ® Build Engine version 15.8.168+ga8fba1ebd7 for .NET Framework”. With this compiler, I often get compiler crash while trying to build SimpleITK’…

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## [New Annotation for Slicer - Splines and Planes](https://discourse.slicer.org/t/new-annotation-for-slicer-splines-and-planes/3951)

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**Author:** [@Johan\_Andruejol](https://discourse.slicer.org/u/Johan_Andruejol)\
**Replies:** 6\
**Last updated:** [September 9, 2018, 12:11pm UTC](https://discourse.slicer.org/t/new-annotation-for-slicer-splines-and-planes/3951 "2018-09-09T12:11:20Z")

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Hi everyone, We have developed new annotation support for Slicer in the form of Splines and Planes. Here is a preview: Planes: Note: Planes annotation are only available in the 3D view Splines: These fulfill t…

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## [Slicer 4.8.1 release and transition to Qt5 and VTK9](https://discourse.slicer.org/t/slicer-4-8-1-release-and-transition-to-qt5-and-vtk9/1551)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 12\
**Last updated:** [January 16, 2018, 11:06pm UTC](https://discourse.slicer.org/t/slicer-4-8-1-release-and-transition-to-qt5-and-vtk9/1551 "2018-01-16T23:06:30Z")

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Hi Slicers, Next week, I suggest we release Slicer 4.8.1 based of the current master. Then, we will toggle the default version of Qt, VTK as well as the C++ version to Qt5, VTK9 and C++11. Let us know what you think.

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## [Does DSCMRIAnalysis module provide leakage correction in making rCBV map?](https://discourse.slicer.org/t/does-dscmrianalysis-module-provide-leakage-correction-in-making-rcbv-map/3971)

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**Author:** [@Kyu\_Sung\_Choi](https://discourse.slicer.org/u/Kyu_Sung_Choi)\
**Replies:** 4\
**Last updated:** [September 7, 2018, 3:41pm UTC](https://discourse.slicer.org/t/does-dscmrianalysis-module-provide-leakage-correction-in-making-rcbv-map/3971 "2018-09-07T15:41:53Z")

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Dear Dr. Fedorov, Thank you for your awesome work on DSCMRIAnalysis module. However, I wonder if DSCMRIAnalysis module provides leakage correction in making rCBV map? I think there’s no motion correction function on D…

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## [DataStore: data not showing for uploaded dataset](https://discourse.slicer.org/t/datastore-data-not-showing-for-uploaded-dataset/175)

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**Author:** [@Lorensen](https://discourse.slicer.org/u/Lorensen)\
**Replies:** 7\
**Last updated:** [September 7, 2018, 10:49am UTC](https://discourse.slicer.org/t/datastore-data-not-showing-for-uploaded-dataset/175 "2018-09-07T10:49:42Z")

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I uploaded an .mrb file to the Slicer datastore rep at: http://slicer.kitware.com/midas3/community/23 And here is the info for the dataset: http://slicer.kitware.com/midas3/item/285338 The data is called Swiss Skull St…

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## [Data Module: column show/hide branch or node is editable](https://discourse.slicer.org/t/data-module-column-show-hide-branch-or-node-is-editable/3992)

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**Author:** [@phcerdan](https://discourse.slicer.org/u/phcerdan)\
**Replies:** 5\
**Last updated:** [September 6, 2018, 6:13pm UTC](https://discourse.slicer.org/t/data-module-column-show-hide-branch-or-node-is-editable/3992 "2018-09-06T18:13:22Z")

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Using a recent Slicer c88b17d38 Is this expected? Thanks

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## [Get each slice of a volume as numpy array](https://discourse.slicer.org/t/get-each-slice-of-a-volume-as-numpy-array/3986)

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**Author:** [@Saima](https://discourse.slicer.org/u/Saima)\
**Replies:** 4\
**Last updated:** [September 5, 2018, 4:26am UTC](https://discourse.slicer.org/t/get-each-slice-of-a-volume-as-numpy-array/3986 "2018-09-05T04:26:02Z")

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## [Multiple extensions failing to build for Mac](https://discourse.slicer.org/t/multiple-extensions-failing-to-build-for-mac/3952)

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**Author:** [@mschumaker](https://discourse.slicer.org/u/mschumaker)\
**Replies:** 1\
**Last updated:** [August 30, 2018, 4:22pm UTC](https://discourse.slicer.org/t/multiple-extensions-failing-to-build-for-mac/3952 "2018-08-30T16:22:38Z")

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I’ve noticed that there are a few extensions on the CDash page for SlicerPreview that fail to build on Mac, and only on Mac. I’m wondering if these problems are related. The extensions that CDash shows are not building …

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## [Saving a VTK model in a certain directory using Python](https://discourse.slicer.org/t/saving-a-vtk-model-in-a-certain-directory-using-python/3946)

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**Author:** [@chaddy1004](https://discourse.slicer.org/u/chaddy1004)\
**Replies:** 2\
**Last updated:** [August 30, 2018, 2:59pm UTC](https://discourse.slicer.org/t/saving-a-vtk-model-in-a-certain-directory-using-python/3946 "2018-08-30T14:59:27Z")

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Hi Is there a way to save a .vtk file in a specific directory using Python? I would like to include this functionality in my script but could not find a good way to do it. Thank you! Chad Paik

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## [Slicer.exe file shuts down when setting the marker](https://discourse.slicer.org/t/slicer-exe-file-shuts-down-when-setting-the-marker/3931)

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**Author:** [@kamrul079](https://discourse.slicer.org/u/kamrul079)\
**Replies:** 5\
**Last updated:** [August 28, 2018, 10:02pm UTC](https://discourse.slicer.org/t/slicer-exe-file-shuts-down-when-setting-the-marker/3931 "2018-08-28T22:02:41Z")

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I had built a module for tracking purpose. it successfully calibrate camera. But when I set the marker setting for the probe tracking, suddenly slicer stops and shuts down with the following error as shown in the image. …

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## [Programming a script to automate Slicer Extension Module for DiceComputation (CLI)](https://discourse.slicer.org/t/programming-a-script-to-automate-slicer-extension-module-for-dicecomputation-cli/3924)

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**Author:** [@phoenixyuwilkie](https://discourse.slicer.org/u/phoenixyuwilkie)\
**Replies:** 5\
**Last updated:** [August 28, 2018, 3:13pm UTC](https://discourse.slicer.org/t/programming-a-script-to-automate-slicer-extension-module-for-dicecomputation-cli/3924 "2018-08-28T15:13:29Z")

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Hello all, I am currently trying to program a script that will automate thresholding of scalar volumes then compute the DSC values of these segmentations when compared with previously manually segmented ones. While the …

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## [Create a volumetric mesh](https://discourse.slicer.org/t/create-a-volumetric-mesh/2931)

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**Author:** [@Hikmat](https://discourse.slicer.org/u/Hikmat)\
**Replies:** 7\
**Last updated:** [May 25, 2018, 7:23pm UTC](https://discourse.slicer.org/t/create-a-volumetric-mesh/2931 "2018-05-25T19:23:24Z")

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Operating system: Windows 10 Slicer version: Slicer 4.8.1 I have clipped a ScalarVolumeNode to define the region of interest. I would now like to create a volumetric mesh from this scalar volume. I am aware of tools an…

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## [BITMAP Exporter](https://discourse.slicer.org/t/bitmap-exporter/3906)

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**Author:** [@Nicholas.jacobson](https://discourse.slicer.org/u/Nicholas.jacobson)\
**Replies:** 1\
**Last updated:** [August 28, 2018, 12:08am UTC](https://discourse.slicer.org/t/bitmap-exporter/3906 "2018-08-28T00:08:15Z")

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Hi all, Looking for a good Bitmap exporter for voxel printing. SlicerFab was good but don’t see it anymore. Any advice?

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## [Disable automatic scene view generation on save](https://discourse.slicer.org/t/disable-automatic-scene-view-generation-on-save/3888)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 14\
**Last updated:** [August 26, 2018, 2:09pm UTC](https://discourse.slicer.org/t/disable-automatic-scene-view-generation-on-save/3888 "2018-08-26T14:09:25Z")

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Currently, a scene view is added on each scene save, which approximately doubles the scene file size, which may be significant when the scene has hundreds of nodes. Also, each time when the scene file is loaded and the …

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## [How to convert model to markups?](https://discourse.slicer.org/t/how-to-convert-model-to-markups/3665)

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**Author:** [@Saha\_Saha](https://discourse.slicer.org/u/Saha_Saha)\
**Replies:** 11\
**Last updated:** [August 13, 2018, 4:10am UTC](https://discourse.slicer.org/t/how-to-convert-model-to-markups/3665 "2018-08-13T04:10:53Z")

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Operating system: window 10 Slicer version: 4.9.0 Expected behavior: Actual behavior: I have dicom data (CT scan) set of spin. Where I need to get point cloud on the surface of vertebra. So I need markups from a mode…

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## [NDI Polaris Spectra connection failed](https://discourse.slicer.org/t/ndi-polaris-spectra-connection-failed/3853)

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**Author:** [@kamrul079](https://discourse.slicer.org/u/kamrul079)\
**Replies:** 1\
**Last updated:** [August 20, 2018, 9:44pm UTC](https://discourse.slicer.org/t/ndi-polaris-spectra-connection-failed/3853 "2018-08-20T21:44:33Z")

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I was trying to connect the NDI spectra with slicer 4.8 build version. I had openIGTLinkIF, slicer 4.8 and pre-build Plus. When I connect the NDI device, it can’t connect with slicer.

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## [Cmake error when building a new C++ loadable extension module](https://discourse.slicer.org/t/cmake-error-when-building-a-new-c-loadable-extension-module/3835)

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**Author:** [@kerry](https://discourse.slicer.org/u/kerry)\
**Replies:** 1\
**Last updated:** [August 20, 2018, 1:00am UTC](https://discourse.slicer.org/t/cmake-error-when-building-a-new-c-loadable-extension-module/3835 "2018-08-20T01:00:50Z")

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Operating system: Windows Slicer version: 4.7 CMake: 3.8.2 I added a new module using the extension manager and the module is set to be a loadable module. Try to build the extension using CMake. The Slicer\_DIR was set…

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## [About resolution of curve maker](https://discourse.slicer.org/t/about-resolution-of-curve-maker/3828)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 1\
**Last updated:** [August 19, 2018, 10:18am UTC](https://discourse.slicer.org/t/about-resolution-of-curve-maker/3828 "2018-08-19T10:18:17Z")

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What I am doing is to get a higher resolution of curve maker, and I changed the code in python just like the picture showing. But there is nothing happen in slicer. Thanks. Li zhenzhu. Binzhou Medical University Hospi…

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## [IGSTK repository can't find for older version of slicer 4.8.1](https://discourse.slicer.org/t/igstk-repository-cant-find-for-older-version-of-slicer-4-8-1/3808)

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**Author:** [@kamrul079](https://discourse.slicer.org/u/kamrul079)\
**Replies:** 7\
**Last updated:** [August 19, 2018, 6:37am UTC](https://discourse.slicer.org/t/igstk-repository-cant-find-for-older-version-of-slicer-4-8-1/3808 "2018-08-19T06:37:48Z")

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I am trying to use webcams or NDI tracking device with my already built module in slicer. I need to build IGSTK. But I could n’t find the repository for IGSTK. I need that version of IGSTK that will compatible with slice…

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## [PlusBuild failed for slicer 4.8.1](https://discourse.slicer.org/t/plusbuild-failed-for-slicer-4-8-1/3825)

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**Author:** [@kamrul079](https://discourse.slicer.org/u/kamrul079)\
**Replies:** 1\
**Last updated:** [August 19, 2018, 12:49am UTC](https://discourse.slicer.org/t/plusbuild-failed-for-slicer-4-8-1/3825 "2018-08-19T00:49:44Z")

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I was trying to build “PlusBuild” for my NDI tracker application. I had already built slicer 4.8.1 from the source. But the Plus 2.6 failed to build in slicer 4.8.1. Does it compatible with this slicer version? Do I ne…

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## [Model slice intersection visibility - only on certain slice views](https://discourse.slicer.org/t/model-slice-intersection-visibility-only-on-certain-slice-views/3807)

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**Author:** [@mschumaker](https://discourse.slicer.org/u/mschumaker)\
**Replies:** 2\
**Last updated:** [August 17, 2018, 4:24pm UTC](https://discourse.slicer.org/t/model-slice-intersection-visibility-only-on-certain-slice-views/3807 "2018-08-17T16:24:11Z")

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I have a 3D model that I would like to display as intersections on some 2D slice views, but hide it on another. I have a vtkMRMLModelNode called arteryModelNode: arteryModelDisplayNode = arteryModelNode.GetModelDisplay…

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## [A user's proposal for Markups Module enhancements](https://discourse.slicer.org/t/a-users-proposal-for-markups-module-enhancements/3362)

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**Author:** [@jclauneuro](https://discourse.slicer.org/u/jclauneuro)\
**Replies:** 20\
**Last updated:** [August 16, 2018, 10:27am UTC](https://discourse.slicer.org/t/a-users-proposal-for-markups-module-enhancements/3362 "2018-08-16T10:27:00Z")

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Dear 3D Slicer Developers, I’ve been a regular user of 3D Slicer for a few years now. In particular, I make use of the Markups Module a fair amount for image fiducial placement. We have protocols in which upwards of 250…

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## [Can Slicer load/save to archives instead of folders, on Mac/Windows?](https://discourse.slicer.org/t/can-slicer-load-save-to-archives-instead-of-folders-on-mac-windows/3785)

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**Author:** [@jdx-john](https://discourse.slicer.org/u/jdx-john)\
**Replies:** 3\
**Last updated:** [August 15, 2018, 5:40pm UTC](https://discourse.slicer.org/t/can-slicer-load-save-to-archives-instead-of-folders-on-mac-windows/3785 "2018-08-15T17:40:05Z")

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I think this is a dev rather than support question - we have a custom Slicer application which saves a plan/project to a single user-specified directory so plans are portable. We also use a traditional “load/save file” a…

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## [No extensions for latest nightly](https://discourse.slicer.org/t/no-extensions-for-latest-nightly/865)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 14\
**Last updated:** [August 13, 2018, 8:02pm UTC](https://discourse.slicer.org/t/no-extensions-for-latest-nightly/865 "2018-08-13T20:02:56Z")

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There are no extensions available for latest nightly version (due to “Variable Slicer\_QT\_VERSION\_MAJOR is not defined” error) and there are also some new failed tests. As about half of the users download the latest nigh…

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## [Error running pip install](https://discourse.slicer.org/t/error-running-pip-install/3822)

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**Author:** [@darekdev](https://discourse.slicer.org/u/darekdev)\
**Replies:** 0\
**Last updated:** [August 13, 2018, 4:12pm UTC](https://discourse.slicer.org/t/error-running-pip-install/3822 "2018-08-13T16:12:50Z")

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I have built Slicer and always have working pip but now module is empty and I can’t run pip.main(\[‘install’, ‘module’\]) \>\>\> import pip \>\>\> pip \<module ‘pip’ from ‘/home/software/medical/slicer4.9/Slicer-SuperBuild-Rel…

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## [How can I display the parametric map from multivolume analysis as a colormap?](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589)

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**Author:** [@Kyu\_Sung\_Choi](https://discourse.slicer.org/u/Kyu_Sung_Choi)\
**Replies:** 11\
**Last updated:** [August 13, 2018, 2:22pm UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589 "2018-08-13T14:22:48Z")

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Dear Dr.Fedorov, Thank you for your awesome work and kind comments. However, I have another question using DSCMRIAnalysis module. How can I display the grayscale rCBV map acquired by DSCMRIAnalysis as a colormap? I o…

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