# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?page=117

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

**Page:** 118

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## [Re-recording the video of " Pedicle Screw Surgical Simulator " from Youtube for users of 3d slicer in China](https://discourse.slicer.org/t/re-recording-the-video-of-pedicle-screw-surgical-simulator-from-youtube-for-users-of-3d-slicer-in-china/3757)

<div class="topic-metadata">

**Author:** [@ezproxy](https://discourse.slicer.org/u/ezproxy)\
**Replies:** 2\
**Last updated:** [August 13, 2018, 1:59pm UTC](https://discourse.slicer.org/t/re-recording-the-video-of-pedicle-screw-surgical-simulator-from-youtube-for-users-of-3d-slicer-in-china/3757 "2018-08-13T13:59:03Z")

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In consideration of China’s Internet environment, many people can’t watch YouTube directly. We’ve Re-recorded the video of " Pedicle Screw Surgical Simulator " from Youtube , labeled the copyright source(3D Slicer中文论坛 E…

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## [How to get brain mask from MR images using skull stripping?](https://discourse.slicer.org/t/how-to-get-brain-mask-from-mr-images-using-skull-stripping/2508)

<div class="topic-metadata">

**Author:** [@Yingli\_Lu](https://discourse.slicer.org/u/Yingli_Lu)\
**Replies:** 3\
**Last updated:** [August 12, 2018, 6:25pm UTC](https://discourse.slicer.org/t/how-to-get-brain-mask-from-mr-images-using-skull-stripping/2508 "2018-08-12T18:25:36Z")

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Hi, OS: Windows 10 slicer: 4.8.1 I have a MR volume: dimensions: 120x256x256 spacing: 1mm x 1mm x 1mm origin: 0mm 0mm 0mm IJK to RAS direction matrix: 0 0 1 0 1 0 1 0 0 after apply skul…

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## [Git-svn commit issue with svn:log line endings](https://discourse.slicer.org/t/git-svn-commit-issue-with-svn-log-line-endings/3728)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 4\
**Last updated:** [August 10, 2018, 9:46pm UTC](https://discourse.slicer.org/t/git-svn-commit-issue-with-svn-log-line-endings/3728 "2018-08-10T21:46:55Z")

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I was trying to commit @Fernando’s pull request but I’m getting this weird error on both linux and mac, even with a fresh checkout. Does anyone know what causes this and how to fix it? $ git svn dcommit --add-author-f…

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## [Building Module in Slicer](https://discourse.slicer.org/t/building-module-in-slicer/3712)

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**Author:** [@kamrul079](https://discourse.slicer.org/u/kamrul079)\
**Replies:** 1\
**Last updated:** [August 8, 2018, 8:37pm UTC](https://discourse.slicer.org/t/building-module-in-slicer/3712 "2018-08-08T20:37:58Z")

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I am developing a 3D slicer module for augmented reality application for the video based navigation system. I had already built slicer 4.8.1 from the source file using Cmake and visual studio 2013 version. I had built sl…

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## [Python debugging in Eclipse](https://discourse.slicer.org/t/python-debugging-in-eclipse/3644)

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**Author:** [@Saima](https://discourse.slicer.org/u/Saima)\
**Replies:** 1\
**Last updated:** [August 3, 2018, 9:38am UTC](https://discourse.slicer.org/t/python-debugging-in-eclipse/3644 "2018-08-03T09:38:33Z")

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Dear Andras, Can you help me with setup IDE liclipse with slicer. I did all the steps. The slicer is connected but when I debug it gives me error. Please see the screen shot below: I dont know what I am doing wrong…

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## [Display color scalar bar matching model scalars](https://discourse.slicer.org/t/display-color-scalar-bar-matching-model-scalars/3620)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [August 2, 2018, 8:35am UTC](https://discourse.slicer.org/t/display-color-scalar-bar-matching-model-scalars/3620 "2018-08-02T08:35:56Z")

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I would like to display a scalar bar that matches the color node/data range of the scalars on a model I am viewing. I can use the colors module to display a scalar bar, but the range is fixed at max… What is the best wa…

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## [Packaged, distributable custom application with a slicelet](https://discourse.slicer.org/t/packaged-distributable-custom-application-with-a-slicelet/3627)

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**Author:** [@mschumaker](https://discourse.slicer.org/u/mschumaker)\
**Replies:** 1\
**Last updated:** [August 1, 2018, 6:28pm UTC](https://discourse.slicer.org/t/packaged-distributable-custom-application-with-a-slicelet/3627 "2018-08-01T18:28:30Z")

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I’d like to create a packaged, distributable application using my slicelet and scripted modules. I’ve looked at the CustomSlicerGenerator, and I know about the work on the SlicerCustomAppTemplate, but with that still in …

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## [Error compiling Qt5 using qt-easy-build/Build-qt.sh script](https://discourse.slicer.org/t/error-compiling-qt5-using-qt-easy-build-build-qt-sh-script/3610)

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**Author:** [@mschumaker](https://discourse.slicer.org/u/mschumaker)\
**Replies:** 6\
**Last updated:** [July 31, 2018, 3:05am UTC](https://discourse.slicer.org/t/error-compiling-qt5-using-qt-easy-build-build-qt-sh-script/3610 "2018-07-31T03:05:13Z")

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@jcfr I’m attempting to build Qt5.10.0 using the qt-easy-build/Build-qt.sh script to deal with the rpath issue with packaging Slicer on Mac, but it fails. Help? Operating system is MacOS 10.12. Xcode 9.2 The Xcode ins…

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## [Building From Source on Ubuntu 16.04 - OpenSSL](https://discourse.slicer.org/t/building-from-source-on-ubuntu-16-04-openssl/1129)

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**Author:** [@codey](https://discourse.slicer.org/u/codey)\
**Replies:** 10\
**Last updated:** [October 9, 2017, 2:12pm UTC](https://discourse.slicer.org/t/building-from-source-on-ubuntu-16-04-openssl/1129 "2017-10-09T14:12:20Z")

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I can build Slicer with the option Slicer\_USE\_PYTHONQT\_WITH\_OPENS off When I try to build with this on I get \[ 11%\] Completed 'bzip2' \[ 12%\] Built target bzip2 \[ 12%\] No configure step for 'OpenSSL' /usr/bin/cmake: l…

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## [Slicer code completion for python](https://discourse.slicer.org/t/slicer-code-completion-for-python/227)

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**Author:** [@brhoom](https://discourse.slicer.org/u/brhoom)\
**Replies:** 3\
**Last updated:** [July 30, 2018, 10:05am UTC](https://discourse.slicer.org/t/slicer-code-completion-for-python/227 "2018-07-30T10:05:53Z")

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Hi, How can I add Slicer libs to LiClipse so I can get some code complettion like the one I get in the debugger. Have a nice weekend!

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## [Slicer packaging Qt5 libraries link](https://discourse.slicer.org/t/slicer-packaging-qt5-libraries-link/3583)

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**Author:** [@juanprietob](https://discourse.slicer.org/u/juanprietob)\
**Replies:** 2\
**Last updated:** [July 26, 2018, 2:12pm UTC](https://discourse.slicer.org/t/slicer-packaging-qt5-libraries-link/3583 "2018-07-26T14:12:31Z")

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Operating system: MACOS 10.13.5 Slicer version: 27287 Expected behavior: Launch Slicer Actual behavior: I have compiled Slicer r 27287 successfully on MACOS high Sierra 10.13.5 The packaging seems to be working afte…

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## [Subject hierarchy listening to events](https://discourse.slicer.org/t/subject-hierarchy-listening-to-events/3364)

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**Author:** [@Johan\_Andruejol](https://discourse.slicer.org/u/Johan_Andruejol)\
**Replies:** 10\
**Last updated:** [July 26, 2018, 7:49pm UTC](https://discourse.slicer.org/t/subject-hierarchy-listening-to-events/3364 "2018-07-26T19:49:43Z")

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Hi all, I am working a module that relies heavily on the subject hierarchy. I need to listen to its modified/added and removed item events. Here is an abstract of what I do: class MyClass(VTKObservationMixin): def \_\_…

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## [VTK 9 in Release 4.8.1](https://discourse.slicer.org/t/vtk-9-in-release-4-8-1/3585)

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**Author:** [@jonieva](https://discourse.slicer.org/u/jonieva)\
**Replies:** 2\
**Last updated:** [July 26, 2018, 4:45pm UTC](https://discourse.slicer.org/t/vtk-9-in-release-4-8-1/3585 "2018-07-26T16:45:04Z")

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Hi there, I am aware that only VTK 9 is supported since Slicer 4.9, but what about the 4.8.1 release? I’m trying to build it with a lower version of VTK and I get the following error: /Users/jonieva/Projects/Slicer/Mod…

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## [Plotting: select point on click?](https://discourse.slicer.org/t/plotting-select-point-on-click/3568)

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**Author:** [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Replies:** 13\
**Last updated:** [July 26, 2018, 2:55pm UTC](https://discourse.slicer.org/t/plotting-select-point-on-click/3568 "2018-07-26T14:55:13Z")

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Is there a plot mode allowing click-to-select a point, rather than dragging the selection box? I only want to select one point at a time. Thanks.

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## [Pip in nightly build not working](https://discourse.slicer.org/t/pip-in-nightly-build-not-working/3325)

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**Author:** [@mcfly3001](https://discourse.slicer.org/u/mcfly3001)\
**Replies:** 6\
**Last updated:** [July 26, 2018, 1:07pm UTC](https://discourse.slicer.org/t/pip-in-nightly-build-not-working/3325 "2018-07-26T13:07:54Z")

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Hi, for another problem I had I was upgrading my Slicer install to the nightly build version. Unfortunately I have problems running the pip installer in the Python Interactive console. I am running the nightly version o…

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## [Nth Fidutial Color](https://discourse.slicer.org/t/nth-fidutial-color/3579)

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**Author:** [@sarafv](https://discourse.slicer.org/u/sarafv)\
**Replies:** 1\
**Last updated:** [July 25, 2018, 9:41pm UTC](https://discourse.slicer.org/t/nth-fidutial-color/3579 "2018-07-25T21:41:07Z")

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Hi, I want to change the color of Nth Fidutial of a vtkMRMLMarkupsFiducialNode on a python script (As in Markups Module =\> Advanced =\> Display Properties =\> Selected Color) I can modify the color of the entired list th…

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## [Python unit test: no startupCompleted signal](https://discourse.slicer.org/t/python-unit-test-no-startupcompleted-signal/3494)

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**Author:** [@Nicole\_Aucoin](https://discourse.slicer.org/u/Nicole_Aucoin)\
**Replies:** 8\
**Last updated:** [July 20, 2018, 1:50pm UTC](https://discourse.slicer.org/t/python-unit-test-no-startupcompleted-signal/3494 "2018-07-20T13:50:55Z")

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I’m updating my python extension from Slicer 4.6 to the master and already fixed it to only use the DICOM database after slicer.app has sent the startupCompleted signal (Modules/Scripted/DICOM/DICOM.py initializes slicer…

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## [Getting a user specified file location](https://discourse.slicer.org/t/getting-a-user-specified-file-location/3530)

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**Author:** [@Troy](https://discourse.slicer.org/u/Troy)\
**Replies:** 1\
**Last updated:** [July 20, 2018, 5:06am UTC](https://discourse.slicer.org/t/getting-a-user-specified-file-location/3530 "2018-07-20T05:06:41Z")

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So I’m writing a program that uploads and reads a file format from the Seimans format (not DICOM), and I need to write a way to have the user find the file location, and then save that location as a string. Pretty much t…

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## [SlicerExtension-VMTK build failing on MacOS 10.12, VTKv9, Qt 5.10](https://discourse.slicer.org/t/slicerextension-vmtk-build-failing-on-macos-10-12-vtkv9-qt-5-10/2650)

<div class="topic-metadata">

**Author:** [@mschumaker](https://discourse.slicer.org/u/mschumaker)\
**Replies:** 26\
**Last updated:** [July 20, 2018, 3:11am UTC](https://discourse.slicer.org/t/slicerextension-vmtk-build-failing-on-macos-10-12-vtkv9-qt-5-10/2650 "2018-07-20T03:11:22Z")

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I’m attempting to build SlicerExtension-VMTK in my Slicer-SuperBuild directory, configuring using CMake 3.11 and using makefiles, and I encounter an error with the VMTK build step: \[ 1%\] Built target vtkvmtkITK make\[5\]…

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## [Uploading a Volume from scratch, but too large a volume causes a crash](https://discourse.slicer.org/t/uploading-a-volume-from-scratch-but-too-large-a-volume-causes-a-crash/3470)

<div class="topic-metadata">

**Author:** [@Troy](https://discourse.slicer.org/u/Troy)\
**Replies:** 4\
**Last updated:** [July 19, 2018, 9:44pm UTC](https://discourse.slicer.org/t/uploading-a-volume-from-scratch-but-too-large-a-volume-causes-a-crash/3470 "2018-07-19T21:44:24Z")

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Hello, I’ve been working on writing a code to read in Seiman’s format PET and CT scans, and I’ve got the majority of the code written. Currently, it reads in PET images with no issues, and I can adjust and view them. How…

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## [Editing Layout through Python script](https://discourse.slicer.org/t/editing-layout-through-python-script/3519)

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**Author:** [@brynpitt](https://discourse.slicer.org/u/brynpitt)\
**Replies:** 2\
**Last updated:** [July 19, 2018, 1:35pm UTC](https://discourse.slicer.org/t/editing-layout-through-python-script/3519 "2018-07-19T13:35:03Z")

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Hello all, I have a very simple problem: I am looking for reference information on changing Slicer’s layout using Python scripts. I know I found such a page in the past (for an older version of Slicer), but I cannot see…

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## [Segment Editor Effect: Fill Between Slices does not recognize existing contour](https://discourse.slicer.org/t/segment-editor-effect-fill-between-slices-does-not-recognize-existing-contour/3452)

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**Author:** [@MRXCAT\_CMR](https://discourse.slicer.org/u/MRXCAT_CMR)\
**Replies:** 9\
**Last updated:** [July 17, 2018, 3:24pm UTC](https://discourse.slicer.org/t/segment-editor-effect-fill-between-slices-does-not-recognize-existing-contour/3452 "2018-07-17T15:24:17Z")

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Operating system: Windows 10 Slicer version: 4.8.1 (r26813) built myself Background: I have started some work on automatic segmentation using the Segment Editor framework. Now I have an automatically generated contour…

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## [Using the OpenIGTLink library in a loadable module](https://discourse.slicer.org/t/using-the-openigtlink-library-in-a-loadable-module/3503)

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**Author:** [@Tiffas](https://discourse.slicer.org/u/Tiffas)\
**Replies:** 2\
**Last updated:** [July 17, 2018, 3:21pm UTC](https://discourse.slicer.org/t/using-the-openigtlink-library-in-a-loadable-module/3503 "2018-07-17T15:21:54Z")

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Hi, I am trying to use the OpenIGTLink library in a C++ module with the following code: igtl::ClientSocket::Pointer socket; socket = igtl::ClientSocket::New(); int r = socket-\>ConnectToServer("172.31.1.2", 18944); I…

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## ["3D Slicer, Python, Xeus and Jupyter" lightning talk at SciPy 2018 conference](https://discourse.slicer.org/t/3d-slicer-python-xeus-and-jupyter-lightning-talk-at-scipy-2018-conference/3482)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 0\
**Last updated:** [July 14, 2018, 3:36am UTC](https://discourse.slicer.org/t/3d-slicer-python-xeus-and-jupyter-lightning-talk-at-scipy-2018-conference/3482 "2018-07-14T03:36:21Z")

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Hi, Currently attending SciPy 2018 conference in Austin, earlier today I was planning on giving the following lightening talk to: introduce the 3D Slicer ecosystem, application and community to the broader Scientific …

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## [vtkMRMLSliceNode observe events](https://discourse.slicer.org/t/vtkmrmlslicenode-observe-events/3480)

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**Author:** [@priya.vada4](https://discourse.slicer.org/u/priya.vada4)\
**Replies:** 2\
**Last updated:** [July 13, 2018, 6:10pm UTC](https://discourse.slicer.org/t/vtkmrmlslicenode-observe-events/3480 "2018-07-13T18:10:16Z")

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Hi I would like to implement custom functionality based on user clicks/keypress in the slice views. I would like to observe the events separately for clicks/keypress in the red and yellow slices. For this, I was impleme…

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## [Pig Spinal Vertebrae Segmentation](https://discourse.slicer.org/t/pig-spinal-vertebrae-segmentation/3476)

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**Author:** [@Hikmat](https://discourse.slicer.org/u/Hikmat)\
**Replies:** 1\
**Last updated:** [July 13, 2018, 1:06am UTC](https://discourse.slicer.org/t/pig-spinal-vertebrae-segmentation/3476 "2018-07-13T01:06:48Z")

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Operating system: Windows 10 Slicer version: 4.8.1 Hi, I am attempting to segment the spinal vertebrae of a pig from CT images. The objective is to generate a surface model from the bone segmentation. The user will t…

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## [Extension not available in Nightly](https://discourse.slicer.org/t/extension-not-available-in-nightly/3469)

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**Author:** [@jonieva](https://discourse.slicer.org/u/jonieva)\
**Replies:** 1\
**Last updated:** [July 12, 2018, 6:13pm UTC](https://discourse.slicer.org/t/extension-not-available-in-nightly/3469 "2018-07-12T18:13:48Z")

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Hi guys, Our Chest\_Imaging\_Platform extension is not available in the Nightly build. I checked the CDash and everything looks fine (http://slicer.cdash.org/index.php?project=Slicer4&filtercount=1&showfilters=1&field1=bu…

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## [Automate "Rotate slice to volume plane" feature in Python](https://discourse.slicer.org/t/automate-rotate-slice-to-volume-plane-feature-in-python/3451)

<div class="topic-metadata">

**Author:** [@cphillips](https://discourse.slicer.org/u/cphillips)\
**Replies:** 2\
**Last updated:** [July 11, 2018, 9:49pm UTC](https://discourse.slicer.org/t/automate-rotate-slice-to-volume-plane-feature-in-python/3451 "2018-07-11T21:49:32Z")

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Is there anyway to automate rotating a slice window? (I.e. automate the clicking of the “rotate to volume plane” button) I have tried: controller = slicer.qMRMLSliceControllerWidget() controller.rotateSliceToBackgroun…

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## [Pending Slicer PRs - MultiVolume hash updates](https://discourse.slicer.org/t/pending-slicer-prs-multivolume-hash-updates/3433)

<div class="topic-metadata">

**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 3\
**Last updated:** [July 9, 2018, 5:23pm UTC](https://discourse.slicer.org/t/pending-slicer-prs-multivolume-hash-updates/3433 "2018-07-09T17:23:29Z")

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There are two trivial PRs that update hashes for the MultiVolume\* components. Can someone please merge, or let me know what is the concern? Unfortunately, I lost my svn password stored in the settings in the process…

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## [Slicer superbuild failing due to out-dated third party libraries: VTK and curl](https://discourse.slicer.org/t/slicer-superbuild-failing-due-to-out-dated-third-party-libraries-vtk-and-curl/3410)

<div class="topic-metadata">

**Author:** [@phcerdan](https://discourse.slicer.org/u/phcerdan)\
**Replies:** 0\
**Last updated:** [July 8, 2018, 4:07am UTC](https://discourse.slicer.org/t/slicer-superbuild-failing-due-to-out-dated-third-party-libraries-vtk-and-curl/3410 "2018-07-08T04:07:07Z")

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Using Archlinux with gcc 8.1.1, the Slicer superbuild with VTKv9 and Qt5 is failing in the following packages: VTK, python, and curl. VTK compiling error is related with HDF5, that has been solved upstream, but Slicer…

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