# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?no_subcategories=false&page=115

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

**Page:** 116

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## [Extract a model from a ROI](https://discourse.slicer.org/t/extract-a-model-from-a-roi/4327)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 1\
**Last updated:** [October 9, 2018, 2:06pm UTC](https://discourse.slicer.org/t/extract-a-model-from-a-roi/4327 "2018-10-09T14:06:02Z")

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In my code I would like to extract the model data within a placed ROI and create two new models from that. Does anybody have any hints or examples on how to achieve this?

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## [Building slicer with system QT](https://discourse.slicer.org/t/building-slicer-with-system-qt/2710)

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**Author:** [@vegoria](https://discourse.slicer.org/u/vegoria)\
**Replies:** 13\
**Last updated:** [October 8, 2018, 12:04pm UTC](https://discourse.slicer.org/t/building-slicer-with-system-qt/2710 "2018-10-08T12:04:59Z")

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Hi, I’m trying to compile slicer for the first time - but when I try to compile QT webkit I get an error: conflicting declaration ‘typedef int32\_t UChar32’ In manual I found information that I can use qt from system pa…

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## [Marching cubes poly result is scaled](https://discourse.slicer.org/t/marching-cubes-poly-result-is-scaled/4280)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 3\
**Last updated:** [October 8, 2018, 7:52am UTC](https://discourse.slicer.org/t/marching-cubes-poly-result-is-scaled/4280 "2018-10-08T07:52:07Z")

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The result of my poly model coming from is not the same scale as my slices. So I am unable to see them overlap and scroll in the 3Dview. Am I missing an extra step? surface = vtk.vtkMarchingCubes() surface.SetInputData(…

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## [Slicer.util.array: format, grayscale and RGB](https://discourse.slicer.org/t/slicer-util-array-format-grayscale-and-rgb/4312)

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**Author:** [@virginia\_fgc](https://discourse.slicer.org/u/virginia_fgc)\
**Replies:** 1\
**Last updated:** [October 8, 2018, 4:03am UTC](https://discourse.slicer.org/t/slicer-util-array-format-grayscale-and-rgb/4312 "2018-10-08T04:03:13Z")

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Hello, I am using the Python console to create a script that handles my imported image as an array thanks to: image = slicer.util.array('T2IMAGE') The image is in an ‘nrrd’ format, and it’s a T2 weighted MR acquisitio…

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## [Link to module library (not logic, mrml, widgets)](https://discourse.slicer.org/t/link-to-module-library-not-logic-mrml-widgets/4291)

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**Author:** [@adamrankin](https://discourse.slicer.org/u/adamrankin)\
**Replies:** 6\
**Last updated:** [October 5, 2018, 7:26pm UTC](https://discourse.slicer.org/t/link-to-module-library-not-logic-mrml-widgets/4291 "2018-10-05T19:26:28Z")

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Hello all, Has anyone linked to a module library? I am trying to call a function in the public interface of the module class, and when I have ... set(MODULE\_TARGET\_LIBRARIES vtkSlicer${MODULE\_NAME}ModuleLogic qSlic…

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## [Creating an array to use in: volumeNode.GetIJKToRASDirections (array)](https://discourse.slicer.org/t/creating-an-array-to-use-in-volumenode-getijktorasdirections-array/4276)

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**Author:** [@Nassir](https://discourse.slicer.org/u/Nassir)\
**Replies:** 2\
**Last updated:** [October 4, 2018, 11:11pm UTC](https://discourse.slicer.org/t/creating-an-array-to-use-in-volumenode-getijktorasdirections-array/4276 "2018-10-04T23:11:56Z")

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Hello, I’m trying to use the function GetIJKToRASDirections on a volume to get its IJK to RAS direction matrix. I previously transformed this image, and will now use the matrix to transform (using the set functions) ano…

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## [Intersection between model and volume to select voxels](https://discourse.slicer.org/t/intersection-between-model-and-volume-to-select-voxels/4256)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 6\
**Last updated:** [October 2, 2018, 2:50pm UTC](https://discourse.slicer.org/t/intersection-between-model-and-volume-to-select-voxels/4256 "2018-10-02T14:50:51Z")

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I have a generated a surface model by applying vtkMarchingCubes on a loaded volume. The next step I would like to perform is to identify which voxels intersect with the triangles that were generated. I was thinking of st…

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## [Problem with version 4.8](https://discourse.slicer.org/t/problem-with-version-4-8/4214)

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**Author:** [@Ash\_Alarfaj](https://discourse.slicer.org/u/Ash_Alarfaj)\
**Replies:** 10\
**Last updated:** [September 28, 2018, 2:28pm UTC](https://discourse.slicer.org/t/problem-with-version-4-8/4214 "2018-09-28T14:28:30Z")

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when I’ve finished the segmentation and need to do the segment statistic. the apply icon didn’t active and I need to save my segmentation then close the programme and reopen it to activate the segment statistic. pleas…

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## [How to implement an extension with one hidden module and one script module ](https://discourse.slicer.org/t/how-to-implement-an-extension-with-one-hidden-module-and-one-script-module/4200)

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**Author:** [@Zhiy](https://discourse.slicer.org/u/Zhiy)\
**Replies:** 2\
**Last updated:** [September 27, 2018, 1:42pm UTC](https://discourse.slicer.org/t/how-to-implement-an-extension-with-one-hidden-module-and-one-script-module/4200 "2018-09-27T13:42:36Z")

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Hi folks, I am implementing an extension with one script module. But some core functions are written by C++. I plan to have one backend loadable module connect to the script module. Anyone has an idea that I can make th…

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## [QtWebEngine dependency](https://discourse.slicer.org/t/qtwebengine-dependency/4195)

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**Author:** [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Replies:** 4\
**Last updated:** [September 27, 2018, 12:54pm UTC](https://discourse.slicer.org/t/qtwebengine-dependency/4195 "2018-09-27T12:54:51Z")

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From 2018.09.18 Hangout - #2 by Sam\_Horvath + :infinity:, QtWebEngine is by far the most brittle, difficult dependency to build, and it’s also the largest single library after SimpleITK (which could potentially be mad…

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## [Adding colors to a volume (painting)](https://discourse.slicer.org/t/adding-colors-to-a-volume-painting/4191)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 6\
**Last updated:** [September 27, 2018, 12:21pm UTC](https://discourse.slicer.org/t/adding-colors-to-a-volume-painting/4191 "2018-09-27T12:21:16Z")

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Hi all, I have a question regarding the editing/ painting of volumes. I would like to craft a color-version of my CT scan and ideally, I would like to follow the following workflow: Load a scan (grayscale) Load a colo…

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## [Rotate volume and get the Quaternion (or Euler)](https://discourse.slicer.org/t/rotate-volume-and-get-the-quaternion-or-euler/4186)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 3\
**Last updated:** [September 27, 2018, 10:08am UTC](https://discourse.slicer.org/t/rotate-volume-and-get-the-quaternion-or-euler/4186 "2018-09-27T10:08:14Z")

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Hello all, In the transform hierarchy of my scene I added a LinearTransfromNode to rotate my volume to its correct pose. In my Python script I would like to get the value of the rotation in quaternion format. I need the…

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## [Slicer logging architecture and flexibility](https://discourse.slicer.org/t/slicer-logging-architecture-and-flexibility/4184)

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**Author:** [@jdx-john](https://discourse.slicer.org/u/jdx-john)\
**Replies:** 1\
**Last updated:** [September 25, 2018, 4:38pm UTC](https://discourse.slicer.org/t/slicer-logging-architecture-and-flexibility/4184 "2018-09-25T16:38:41Z")

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Hi, in our commercial project we are finding that default Slicer logging is pretty difficult for our users. Our app-specific logs like “Procedure initiated…” get lost amongst all the internal logging. Users struggle to i…

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## [Newbie question on using filters and access imagedata](https://discourse.slicer.org/t/newbie-question-on-using-filters-and-access-imagedata/3978)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 2\
**Last updated:** [September 25, 2018, 1:41pm UTC](https://discourse.slicer.org/t/newbie-question-on-using-filters-and-access-imagedata/3978 "2018-09-25T13:41:13Z")

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Hi all, I am working on a module for exporting image data from slicer to a format for our medical simulation systems. I have started with a simple python module for thresholding, scaling and normalizing the data (0 – 1)…

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## [Get world coordinate of maximum intensity voxel](https://discourse.slicer.org/t/get-world-coordinate-of-maximum-intensity-voxel/4168)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 3\
**Last updated:** [September 23, 2018, 10:37pm UTC](https://discourse.slicer.org/t/get-world-coordinate-of-maximum-intensity-voxel/4168 "2018-09-23T22:37:57Z")

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Hi Dear Developers and Users I want to create sphere model centerd in the voxel with maximum value. Steps: 1- Load PET images using “DICOM Browser”. 2- Click on “Center Volume” in the module of “Volumes”. 3- Enter …

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## [Profiling 3DSlicer](https://discourse.slicer.org/t/profiling-3dslicer/4161)

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**Author:** [@Davide\_Punzo](https://discourse.slicer.org/u/Davide_Punzo)\
**Replies:** 3\
**Last updated:** [September 21, 2018, 4:18pm UTC](https://discourse.slicer.org/t/profiling-3dslicer/4161 "2018-09-21T16:18:21Z")

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Hi all, I need to properly profile the CPU and RAM usage of 3DSlicer. I tried few tools on windows like VS, C++ memory validator and mtuner. To these software you can give just the binaries, they will start it, then you…

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## [Apply filters on vtkMRMLVolumeNode and then display the filtered volume in Slicer](https://discourse.slicer.org/t/apply-filters-on-vtkmrmlvolumenode-and-then-display-the-filtered-volume-in-slicer/1569)

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**Author:** [@urbancsaba](https://discourse.slicer.org/u/urbancsaba)\
**Replies:** 15\
**Last updated:** [September 21, 2018, 7:45am UTC](https://discourse.slicer.org/t/apply-filters-on-vtkmrmlvolumenode-and-then-display-the-filtered-volume-in-slicer/1569 "2018-09-21T07:45:36Z")

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Hi All, I have a custom loadable modul. In this modul, I want to apply IKT or VTK filters on the previously loaded DICOM volume. I have something like this: vtkMRMLVolumeNode\* volumeNode = d-\>MRMLVolumeNode; // this co…

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## [Surgical tool tracking using NDI polaris and 3D Slicer](https://discourse.slicer.org/t/surgical-tool-tracking-using-ndi-polaris-and-3d-slicer/4157)

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**Author:** [@kamrul079](https://discourse.slicer.org/u/kamrul079)\
**Replies:** 6\
**Last updated:** [September 20, 2018, 5:15pm UTC](https://discourse.slicer.org/t/surgical-tool-tracking-using-ndi-polaris-and-3d-slicer/4157 "2018-09-20T17:15:13Z")

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How to do this type of work in 3d slicer using PLUS toolkit? Is there any step by step procedures?

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## [Creating a 3D slicer module that keeps running](https://discourse.slicer.org/t/creating-a-3d-slicer-module-that-keeps-running/4149)

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**Author:** [@JuanTelo](https://discourse.slicer.org/u/JuanTelo)\
**Replies:** 1\
**Last updated:** [September 19, 2018, 1:37pm UTC](https://discourse.slicer.org/t/creating-a-3d-slicer-module-that-keeps-running/4149 "2018-09-19T13:37:33Z")

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Operating system: Windows Slicer version: 4.8.1 Hi I’m new to developing with 3D slicer and I want to know if it’s possible to create a module that does not stop running, that is, keeps running in the background while …

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## [Adding a python package to an extension/custom Slicer](https://discourse.slicer.org/t/adding-a-python-package-to-an-extension-custom-slicer/4145)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [September 18, 2018, 5:33pm UTC](https://discourse.slicer.org/t/adding-a-python-package-to-an-extension-custom-slicer/4145 "2018-09-18T17:33:16Z")

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I need to add a python package (girder\_client) to a custom Slicer version I am working on. With the current difficulties in using pip in Slicer, I wanted to have it added during the build. Does anyone have an example/…

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## [Build error: class vtkCellPicker has no member named Pick3DPoint](https://discourse.slicer.org/t/build-error-class-vtkcellpicker-has-no-member-named-pick3dpoint/4141)

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**Author:** [@zhaobingshuai](https://discourse.slicer.org/u/zhaobingshuai)\
**Replies:** 1\
**Last updated:** [September 18, 2018, 1:13pm UTC](https://discourse.slicer.org/t/build-error-class-vtkcellpicker-has-no-member-named-pick3dpoint/4141 "2018-09-18T13:13:40Z")

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make -j4 when i use this command,i meet the following error: \[ 33%\] Linking CXX shared library …/…/bin/libSlicerBaseLogicPythonD.so Libs/MRML/DisplayableManager/CMakeFiles/MRMLDisplayableManager.dir/build.make:7…

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## [How to handle images defined in left-handed coordinate system](https://discourse.slicer.org/t/how-to-handle-images-defined-in-left-handed-coordinate-system/4133)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 5\
**Last updated:** [September 18, 2018, 6:12am UTC](https://discourse.slicer.org/t/how-to-handle-images-defined-in-left-handed-coordinate-system/4133 "2018-09-18T06:12:49Z")

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Small aside on this - the voxel-to-physical coordinate system that describes acquisition geometry can be left handed (e.g. axial foot-first vs head-first). ITK readers re-arrange the data to enforce right-handedness. V…

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## [Automate loading, editing and exporting with no user interaction](https://discourse.slicer.org/t/automate-loading-editing-and-exporting-with-no-user-interaction/4129)

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**Author:** [@javi0unavailable](https://discourse.slicer.org/u/javi0unavailable)\
**Replies:** 1\
**Last updated:** [September 17, 2018, 4:27am UTC](https://discourse.slicer.org/t/automate-loading-editing-and-exporting-with-no-user-interaction/4129 "2018-09-17T04:27:11Z")

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Greetings. I want to help a doctor friend to achieve what the title says. I have no idea from medical argot but I know about software development. Basically what I need is to know the easiest way to automate a few step…

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## [2018.09.16: Expect delayed nightly Slicer installers and extensions](https://discourse.slicer.org/t/2018-09-16-expect-delayed-nightly-slicer-installers-and-extensions/4125)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 0\
**Last updated:** [September 16, 2018, 10:13am UTC](https://discourse.slicer.org/t/2018-09-16-expect-delayed-nightly-slicer-installers-and-extensions/4125 "2018-09-16T10:13:37Z")

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Similarly to the other day \[1\], we are finalizing work related to an other project and are using the Slicer build infrastructure. This means the Slicer packages and associated extensions will be available later today or…

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## [Improve the resolution of segment for "import a model"](https://discourse.slicer.org/t/improve-the-resolution-of-segment-for-import-a-model/4030)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 6\
**Last updated:** [September 15, 2018, 12:39pm UTC](https://discourse.slicer.org/t/improve-the-resolution-of-segment-for-import-a-model/4030 "2018-09-15T12:39:15Z")

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What I am doing is to have a boolean opertation between two cylinder created by MakerupToModel. But the segment resolution seems not very well even after “crop volume wih 0.01 spacing scale” just as suggestion: Segmenta…

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## [Extract point data from label map in CLI module](https://discourse.slicer.org/t/extract-point-data-from-label-map-in-cli-module/405)

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**Author:** [@DanC](https://discourse.slicer.org/u/DanC)\
**Replies:** 11\
**Last updated:** [September 15, 2018, 9:28am UTC](https://discourse.slicer.org/t/extract-point-data-from-label-map-in-cli-module/405 "2018-09-15T09:28:27Z")

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Hi all. I would like to extract the point data from a 3d label map in a CLI module. Seems I could save to nrrd -\> open with itkreader -\> iterate over voxels and find filled voxels. Is there a way to directly get the dat…

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## [How to select segment](https://discourse.slicer.org/t/how-to-select-segment/4120)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 4\
**Last updated:** [September 15, 2018, 8:51am UTC](https://discourse.slicer.org/t/how-to-select-segment/4120 "2018-09-15T08:51:45Z")

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I have two segment “skin1” and “skin2”. And when I apply threshold with CLI, I donot know how to select the second one. I don’t know how to set parameters for skin2 # Thresholding segmentEditorWidget.setActiveEffectBy…

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## [2018.09.13: Only nightly Slicer packages - do not expect extensions this morning](https://discourse.slicer.org/t/2018-09-13-only-nightly-slicer-packages-do-not-expect-extensions-this-morning/4097)

<div class="topic-metadata">

**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 5\
**Last updated:** [September 14, 2018, 2:11pm UTC](https://discourse.slicer.org/t/2018-09-13-only-nightly-slicer-packages-do-not-expect-extensions-this-morning/4097 "2018-09-14T14:11:52Z")

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Dear Slicers, Exceptionally, we need to use the Slicer build infrastructure for supporting an other project. (Usually, we rely on the spare cycle of the infrastructure to support other projects) This means: you shoul…

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## [\`import dicom\` resolves differently across platforms](https://discourse.slicer.org/t/import-dicom-resolves-differently-across-platforms/4072)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 11\
**Last updated:** [September 12, 2018, 12:41pm UTC](https://discourse.slicer.org/t/import-dicom-resolves-differently-across-platforms/4072 "2018-09-12T12:41:50Z")

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It appears that import dicom works inconsistently across platforms, perhaps this is due to runtime load ordering issues: mac (resolves to pydicom): \>\>\> import dicom \>\>\> print dicom \<module 'dicom' from '/Applications/S…

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## [Document modules on readthedocs](https://discourse.slicer.org/t/document-modules-on-readthedocs/330)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 27\
**Last updated:** [September 11, 2018, 10:18pm UTC](https://discourse.slicer.org/t/document-modules-on-readthedocs/330 "2018-09-11T22:18:07Z")

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I quite like the Slicer documentation on readthedocs. I would like to try to write documentation for the Segment editor module there. @jcfr How can I contribute? Should I push changes into the rst-user-and-dev-guide br…

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