# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?no_subcategories=false&page=91

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

**Page:** 92

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## [Automated Spinal Cord Segmentation](https://discourse.slicer.org/t/automated-spinal-cord-segmentation/3161)

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**Author:** [@Hikmat](https://discourse.slicer.org/u/Hikmat)\
**Replies:** 10\
**Last updated:** [July 3, 2020, 7:14pm UTC](https://discourse.slicer.org/t/automated-spinal-cord-segmentation/3161 "2020-07-03T19:14:05Z")

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Slicer version: 4.8.1 Hi, I am aiming to automate spinal cord segmentation from MR images. I have been using Spinal Cord Toolbox (SCT); a Linux-based open-source software dedicated specifically to the processing and an…

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## [Publish an extension without building Slicer](https://discourse.slicer.org/t/publish-an-extension-without-building-slicer/12348)

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**Author:** [@TiphaineJh](https://discourse.slicer.org/u/TiphaineJh)\
**Replies:** 1\
**Last updated:** [July 2, 2020, 7:40pm UTC](https://discourse.slicer.org/t/publish-an-extension-without-building-slicer/12348 "2020-07-02T19:40:06Z")

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Hello, I am currently developping a python module in slicer 4.11.0 and would like to publish it to the Extensions Catalog of Slicer. I would like to know if I have to build slicer in order to publish it, and if there i…

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## [Python Library for Local Threshold Effect](https://discourse.slicer.org/t/python-library-for-local-threshold-effect/12345)

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**Author:** [@vertebra](https://discourse.slicer.org/u/vertebra)\
**Replies:** 1\
**Last updated:** [July 2, 2020, 7:35pm UTC](https://discourse.slicer.org/t/python-library-for-local-threshold-effect/12345 "2020-07-02T19:35:36Z")

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In Python through slicer, is there a way to run the local threshold effect like the following pseudocode? set feature size to 6.000 mm set threshold range to 245.00 to 1003.00 set type to grow cut segment = point.loc…

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## [Loading DICOM frames as volume](https://discourse.slicer.org/t/loading-dicom-frames-as-volume/12301)

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**Author:** [@mjg](https://discourse.slicer.org/u/mjg)\
**Replies:** 6\
**Last updated:** [July 1, 2020, 3:53pm UTC](https://discourse.slicer.org/t/loading-dicom-frames-as-volume/12301 "2020-07-01T15:53:39Z")

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Hello, I am trying to load in DICOM frames as a volume; there is no change in position but they are taken at different times to see cardiac muscle contraction. I can’t seem to load the set as a volume through any Slicer…

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## [Python API documentation?](https://discourse.slicer.org/t/python-api-documentation/12298)

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**Author:** [@joachim](https://discourse.slicer.org/u/joachim)\
**Replies:** 3\
**Last updated:** [June 30, 2020, 4:15pm UTC](https://discourse.slicer.org/t/python-api-documentation/12298 "2020-06-30T16:15:17Z")

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Is there an API documentation for the Python interface of Slicer? I haven’t found it. What I’ve found is the C++ documentation, and I use this when I try to do Python. I guess the Python interface is generated from C++ …

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## [Import Nrrd files with color](https://discourse.slicer.org/t/import-nrrd-files-with-color/12283)

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**Author:** [@Niels](https://discourse.slicer.org/u/Niels)\
**Replies:** 1\
**Last updated:** [June 29, 2020, 8:27pm UTC](https://discourse.slicer.org/t/import-nrrd-files-with-color/12283 "2020-06-29T20:27:17Z")

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I have some nrrd files which contain color. So the typical header looks like this: dimension: 4 sizes: 3 50 50 47 However i am unable to import the information in slicer. Should i alter the header? Or use some other w…

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## [Alter number of points which makes up VTK curve](https://discourse.slicer.org/t/alter-number-of-points-which-makes-up-vtk-curve/12273)

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**Author:** [@mjg](https://discourse.slicer.org/u/mjg)\
**Replies:** 3\
**Last updated:** [June 29, 2020, 6:29pm UTC](https://discourse.slicer.org/t/alter-number-of-points-which-makes-up-vtk-curve/12273 "2020-06-29T18:29:59Z")

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Hello, Is there some way to take an existing Slicer VTK curve node, say it is defined by 4 initial points I have placed, and increase the number of points along the curve to be a number such as 100, such that the curve …

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## [Editing endpoints in extract centerline module by Python scripting](https://discourse.slicer.org/t/editing-endpoints-in-extract-centerline-module-by-python-scripting/12250)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 3\
**Last updated:** [June 28, 2020, 2:22pm UTC](https://discourse.slicer.org/t/editing-endpoints-in-extract-centerline-module-by-python-scripting/12250 "2020-06-28T14:22:08Z")

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Hello Everyone, Currently, the extract centerline module allows the removal of branches by clicking on the endpoints. I would like to know if it’s possible to do the same task using a set of input coordinates (coordina…

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## [Calling Python from C++](https://discourse.slicer.org/t/calling-python-from-c/7841)

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**Author:** [@rprueckl](https://discourse.slicer.org/u/rprueckl)\
**Replies:** 9\
**Last updated:** [June 26, 2020, 3:14pm UTC](https://discourse.slicer.org/t/calling-python-from-c/7841 "2020-06-26T15:14:44Z")

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Hi, as the title suggests, the question is whether there is a possibility to call a scripted python module from C++, and if yes, how to do that.

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## [Can I read the transform calculated from elastix](https://discourse.slicer.org/t/can-i-read-the-transform-calculated-from-elastix/12191)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 6\
**Last updated:** [June 26, 2020, 2:24pm UTC](https://discourse.slicer.org/t/can-i-read-the-transform-calculated-from-elastix/12191 "2020-06-26T14:24:11Z")

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I’d like to add an already calculated elastix transform file(txt) to Slicer. However, when I try to add the file to Slicer using the “Add Data” screen, it fails almost silently.

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## [Enforcing same orientation of image every time](https://discourse.slicer.org/t/enforcing-same-orientation-of-image-every-time/12223)

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**Author:** [@rohan\_n](https://discourse.slicer.org/u/rohan_n)\
**Replies:** 1\
**Last updated:** [June 26, 2020, 2:25am UTC](https://discourse.slicer.org/t/enforcing-same-orientation-of-image-every-time/12223 "2020-06-26T02:25:24Z")

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For a Python scripted module, I am loading a series of DICOM images for a DCE MR image into a volume with this syntax: plugin = slicer.modules.dicomPlugins\['DICOMScalarVolumePlugin'\]() loadables = plugin.examine(\[files\]…

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## [Slice cropped as volume](https://discourse.slicer.org/t/slice-cropped-as-volume/12194)

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**Author:** [@ada](https://discourse.slicer.org/u/ada)\
**Replies:** 1\
**Last updated:** [June 25, 2020, 9:22pm UTC](https://discourse.slicer.org/t/slice-cropped-as-volume/12194 "2020-06-25T21:22:02Z")

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Hi all, I have a 3D volume and I would like to display the ‘Red’ slice view. In python, it is working using : red = slicer.util.getNode(‘vtkMRMLSliceNodeRed’) red.SetSliceVisible(1) Nevertheless the slice is extende…

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## [Creating a 3D image from a stack of contours](https://discourse.slicer.org/t/creating-a-3d-image-from-a-stack-of-contours/12217)

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**Author:** [@loubna](https://discourse.slicer.org/u/loubna)\
**Replies:** 3\
**Last updated:** [June 25, 2020, 5:18pm UTC](https://discourse.slicer.org/t/creating-a-3d-image-from-a-stack-of-contours/12217 "2020-06-25T17:18:09Z")

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I’m trying to create a 3D labelMa from a stack of 2D contours in SlicerRT. . My idea is to binarize the contours, and to run a marching cubes on the resulting binary volume. Before do that. I have Added some treatments w…

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## [Windows debug build and python library](https://discourse.slicer.org/t/windows-debug-build-and-python-library/12207)

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**Author:** [@finetjul](https://discourse.slicer.org/u/finetjul)\
**Replies:** 2\
**Last updated:** [June 24, 2020, 10:57pm UTC](https://discourse.slicer.org/t/windows-debug-build-and-python-library/12207 "2020-06-24T22:57:10Z")

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Hi all, What is the status with debug build of Slicer on Windows ? I am trying to build Slicer master (without SimpleITK) on MSVC2017 x64 in Debug with no luck. I saw some recent changes from @lassoan. e.g. 49f3f0b8. A…

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## [Fail to load OpenIGTLinkIF](https://discourse.slicer.org/t/fail-to-load-openigtlinkif/12185)

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**Author:** [@kobidk](https://discourse.slicer.org/u/kobidk)\
**Replies:** 3\
**Last updated:** [June 24, 2020, 2:25pm UTC](https://discourse.slicer.org/t/fail-to-load-openigtlinkif/12185 "2020-06-24T14:25:36Z")

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Operating system:Windows Slicer version:4.10.2 Expected behavior: Load OpenIGTLinkIF Actual behavior: Doesn’t appear in the Slicer menu “modules” list, after loading it as a package using Extention Manager.

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## [My QActions hangs the Slicer application](https://discourse.slicer.org/t/my-qactions-hangs-the-slicer-application/12152)

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**Author:** [@joachim](https://discourse.slicer.org/u/joachim)\
**Replies:** 3\
**Last updated:** [June 23, 2020, 6:37pm UTC](https://discourse.slicer.org/t/my-qactions-hangs-the-slicer-application/12152 "2020-06-23T18:37:30Z")

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I’m creating 2 layouts for manual segmentation. And I’m trying to create QtAction s to trigger these layouts (slicerrc.py-file can be found here): # XML definitions (definitions omitted) LAYOUTXML\_MANUALSEGMENTATION\_3D …

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## [\[Windows\] Debug SimpleITK build failed](https://discourse.slicer.org/t/windows-debug-simpleitk-build-failed/11914)

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**Author:** [@adamrankin](https://discourse.slicer.org/u/adamrankin)\
**Replies:** 6\
**Last updated:** [June 23, 2020, 1:04am UTC](https://discourse.slicer.org/t/windows-debug-simpleitk-build-failed/11914 "2020-06-23T01:04:15Z")

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Hello all, My debug build of Slicer fails on SimpleITK looking for python36\_d.lib, is this a known issue? I’ve scanned https://discourse.slicer.org/t/3d-slicer-windows-10-build-fail-only-simpleitk-project/6727/25 and t…

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## [Recover 2d curve from 2d slices](https://discourse.slicer.org/t/recover-2d-curve-from-2d-slices/12160)

<div class="topic-metadata">

**Author:** [@loubna](https://discourse.slicer.org/u/loubna)\
**Replies:** 4\
**Last updated:** [June 22, 2020, 6:13pm UTC](https://discourse.slicer.org/t/recover-2d-curve-from-2d-slices/12160 "2020-06-22T18:13:57Z")

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Hi, Is there any way to recover the points of 2D curve corresponding to segmented area into 2D slices as shown in figure. I want recover the coordinates of red points (red curve) surrounded the green area. I know that …

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## [Build fails in vtkExodus on Linux](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 13\
**Last updated:** [June 22, 2020, 5:46pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018 "2020-06-22T17:46:54Z")

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Hello, After today’s pull, build fails on Linux with these messages : /usr/bin/ld: CMakeFiles/vtkexodusII.dir/src/ex\_open\_par.c.o:(.rodata+0x0): multiple definition of \`exodus\_unused\_symbol\_dummy\_1’; CMakeFiles/vtkexo…

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## [Entension "SlicerVideoCameras" Loading problem](https://discourse.slicer.org/t/entension-slicervideocameras-loading-problem/12149)

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**Author:** [@endlessric23](https://discourse.slicer.org/u/endlessric23)\
**Replies:** 0\
**Last updated:** [June 22, 2020, 7:53am UTC](https://discourse.slicer.org/t/entension-slicervideocameras-loading-problem/12149 "2020-06-22T07:53:32Z")

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Dear Slicer’s user: I download the Entension “SlicerVideoCameras”, but after I download this, I couldn’t see the extension in my library,there might be some error here.Is there any error in the code or am I doing somet…

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## [MIPs using reslice.SetSlabModeToMax()](https://discourse.slicer.org/t/mips-using-reslice-setslabmodetomax/12104)

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**Author:** [@rohan\_n](https://discourse.slicer.org/u/rohan_n)\
**Replies:** 1\
**Last updated:** [June 20, 2020, 4:43am UTC](https://discourse.slicer.org/t/mips-using-reslice-setslabmodetomax/12104 "2020-06-20T04:43:59Z")

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Can someone please explain how the SetSlabNumberOfSlices feature works for displaying MIPs as shown here: https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Thick\_slab\_reconstruction\_and\_maximum.2Fminimu…

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## [2020.06.09: macOS packages will \*not\* be available until build machine is updated to macOS 10.13.6](https://discourse.slicer.org/t/2020-06-09-macos-packages-will-not-be-available-until-build-machine-is-updated-to-macos-10-13-6/11935)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 17\
**Last updated:** [June 20, 2020, 2:48am UTC](https://discourse.slicer.org/t/2020-06-09-macos-packages-will-not-be-available-until-build-machine-is-updated-to-macos-10-13-6/11935 "2020-06-20T02:48:38Z")

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Tomorrow, we plan to initiate the update the build machine responsible to build: Slicer macOS application installer distributed on https://download.slicer.org corresponding Slicer extensions Implications for users Pr…

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## [Debugging a Loadable Extension (Linux)](https://discourse.slicer.org/t/debugging-a-loadable-extension-linux/12122)

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**Author:** [@nsbosse](https://discourse.slicer.org/u/nsbosse)\
**Replies:** 3\
**Last updated:** [June 19, 2020, 9:53pm UTC](https://discourse.slicer.org/t/debugging-a-loadable-extension-linux/12122 "2020-06-19T21:53:11Z")

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OS: Linux CentOS 8 Slicer git tag: 80f7a47e343266b5ca7cca59a09816fbbdd6101a Hi there, I’m working on a loadable extension with a custom Slicer build made using SlicerCAT. I’m able to debug my extension by using “./Slic…

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## [Do we want to swap bottom viewers in four-up layout?](https://discourse.slicer.org/t/do-we-want-to-swap-bottom-viewers-in-four-up-layout/12096)

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**Author:** [@ungi](https://discourse.slicer.org/u/ungi)\
**Replies:** 4\
**Last updated:** [June 19, 2020, 1:12pm UTC](https://discourse.slicer.org/t/do-we-want-to-swap-bottom-viewers-in-four-up-layout/12096 "2020-06-19T13:12:03Z")

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I find myself often swapping the bottom 2D views in default four-up layout. Currently, sagittal plane is displayed under axial by default. But it can be more intuitive to have the coronal plane under axial, and sagittal …

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## [Markups module confusion - suggestions to improve](https://discourse.slicer.org/t/markups-module-confusion-suggestions-to-improve/12075)

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**Author:** [@ddrobny](https://discourse.slicer.org/u/ddrobny)\
**Replies:** 5\
**Last updated:** [June 18, 2020, 8:34pm UTC](https://discourse.slicer.org/t/markups-module-confusion-suggestions-to-improve/12075 "2020-06-18T20:34:33Z")

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Hi, I’d like to describe my experience with the Slicer markups module and suggest some improvements. I wanted to place some fiducials and export them as a list. I opened the Markups module and click the first icon “Cre…

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## [Automate Fiducial Registration](https://discourse.slicer.org/t/automate-fiducial-registration/3061)

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**Author:** [@Hikmat](https://discourse.slicer.org/u/Hikmat)\
**Replies:** 7\
**Last updated:** [October 16, 2018, 4:43pm UTC](https://discourse.slicer.org/t/automate-fiducial-registration/3061 "2018-10-16T16:43:58Z")

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Operating system: Windows 10 Slicer version: Slicer 4.8.1 Hi, I am writing a simulator which requires the registration of CT and MRI images. I am satisfied with Fiducial Registration; however, the steps required to pe…

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## [Adjust volume rendering transfer function in Python](https://discourse.slicer.org/t/adjust-volume-rendering-transfer-function-in-python/12069)

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**Author:** [@Dootsiie](https://discourse.slicer.org/u/Dootsiie)\
**Replies:** 1\
**Last updated:** [June 17, 2020, 12:27pm UTC](https://discourse.slicer.org/t/adjust-volume-rendering-transfer-function-in-python/12069 "2020-06-17T12:27:21Z")

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Hi, I tried adjusting the transfer function on a 3D volume by using the lines of code you mentioned here. However, I do not see any difference in the 3D volume. Can you help me out? What I did, is I loaded the volume, v…

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## [How to set volume rendering preset using Python](https://discourse.slicer.org/t/how-to-set-volume-rendering-preset-using-python/3063)

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**Author:** [@ollih10](https://discourse.slicer.org/u/ollih10)\
**Replies:** 8\
**Last updated:** [August 1, 2019, 4:06am UTC](https://discourse.slicer.org/t/how-to-set-volume-rendering-preset-using-python/3063 "2019-08-01T04:06:08Z")

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Hi developers, Using a Python script I am trying to load a volume, set the slice views and also a volume rendering preset. While loading and setting the slice views works out well, the volume rendering always shows up w…

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## [Restarting slicer to load loadable module](https://discourse.slicer.org/t/restarting-slicer-to-load-loadable-module/12053)

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**Author:** [@fpsiddiqui91](https://discourse.slicer.org/u/fpsiddiqui91)\
**Replies:** 1\
**Last updated:** [June 16, 2020, 11:51am UTC](https://discourse.slicer.org/t/restarting-slicer-to-load-loadable-module/12053 "2020-06-16T11:51:49Z")

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Dear all, I have been working with slicer modules for a couple of months now. I think there has already been a solution to this which I might have missed. I am working with a custom C++ loadable module, do I have to re…

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## [Build fails in python-ensurepip on Linux](https://discourse.slicer.org/t/build-fails-in-python-ensurepip-on-linux/12023)

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**Author:** [@Zerfox](https://discourse.slicer.org/u/Zerfox)\
**Replies:** 3\
**Last updated:** [June 15, 2020, 8:44pm UTC](https://discourse.slicer.org/t/build-fails-in-python-ensurepip-on-linux/12023 "2020-06-15T20:44:41Z")

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Hi! I am trying to build the nightly version of Slicer on Arch Linux (5.7.2-arch1-1) in debug mode using the developers instructions. During the install step for ‘python-ensurepip’ I get the following error: \[ 59%\] Pe…

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