# Development

**URL:** https://discourse.slicer.org/c/dev/5.md?no_subcategories=false&page=9

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

**Page:** 10

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## [Do you know how to convert real world coordination to image coordination?](https://discourse.slicer.org/t/do-you-know-how-to-convert-real-world-coordination-to-image-coordination/41748)

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**Author:** [@chris\_Prince](https://discourse.slicer.org/u/chris_Prince)\
**Replies:** 1\
**Last updated:** [February 17, 2025, 9:35pm UTC](https://discourse.slicer.org/t/do-you-know-how-to-convert-real-world-coordination-to-image-coordination/41748 "2025-02-17T21:35:35Z")

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In data probe. we can see the image coordination, do you know or having script to know how it convert the real world coordination to image coordination? My task is to get the boundingbox in 2D slicer from 3D segmenta…

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## [Extract brain cavity using script](https://discourse.slicer.org/t/extract-brain-cavity-using-script/17270)

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**Author:** [@park](https://discourse.slicer.org/u/park)\
**Replies:** 1\
**Last updated:** [February 15, 2025, 6:10pm UTC](https://discourse.slicer.org/t/extract-brain-cavity-using-script/17270 "2025-02-15T18:10:35Z")

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Hi everyone I would like to extract the cavity of brain space using “Wrap solidify” and Python script. This is my code to implement what I thought Before performing the “Wrap solidify”, the segmentation using "Thresho…

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## [Help with 3D Model Registration to Patient’s Face for Image-Guided Surgery in 3D Slicer](https://discourse.slicer.org/t/help-with-3d-model-registration-to-patient-s-face-for-image-guided-surgery-in-3d-slicer/41670)

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**Author:** [@Navneet](https://discourse.slicer.org/u/Navneet)\
**Replies:** 2\
**Last updated:** [February 14, 2025, 7:06am UTC](https://discourse.slicer.org/t/help-with-3d-model-registration-to-patient-s-face-for-image-guided-surgery-in-3d-slicer/41670 "2025-02-14T07:06:28Z")

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Hello everyone, I am working on an image-guided surgery project using 3D Slicer, where I need to register a 3D MRI model to a patient’s face in real time. The goal is to track the patient’s face using a webcam and marke…

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## [Matlab -- Slicer](https://discourse.slicer.org/t/matlab-slicer/41688)

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**Author:** [@Fayez](https://discourse.slicer.org/u/Fayez)\
**Replies:** 1\
**Last updated:** [February 14, 2025, 3:01am UTC](https://discourse.slicer.org/t/matlab-slicer/41688 "2025-02-14T03:01:23Z")

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Hi Everyone, I have a matlab script that reads and import data into matlab. I want to load these files from matlab script into slider environment via the matlab code. Is this possible ? Thanks

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## [Safe way to handle QT events](https://discourse.slicer.org/t/safe-way-to-handle-qt-events/41686)

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**Author:** [@DouSam](https://discourse.slicer.org/u/DouSam)\
**Replies:** 1\
**Last updated:** [February 13, 2025, 8:21pm UTC](https://discourse.slicer.org/t/safe-way-to-handle-qt-events/41686 "2025-02-13T20:21:26Z")

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We are working on the TutorialMaker extension. One of the processes is to execute the tutorial, you can see one here. The idea is to recreate the steps like a user normally does and take a screenshot after this step, bu…

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## [MONAILABEL all organs segmentation](https://discourse.slicer.org/t/monailabel-all-organs-segmentation/41682)

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**Author:** [@Maria\_Bota](https://discourse.slicer.org/u/Maria_Bota)\
**Replies:** 0\
**Last updated:** [February 13, 2025, 4:08pm UTC](https://discourse.slicer.org/t/monailabel-all-organs-segmentation/41682 "2025-02-13T16:08:43Z")

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Hello, I am runing the Monailabel radiology app inference. I want to be able to run inference just for a specific organ(e.g aorta) without looking for all organs. Is it possible to select the organ before running infere…

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## [Build errors with slicer (error LNK2005)](https://discourse.slicer.org/t/build-errors-with-slicer-error-lnk2005/36956)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 1\
**Last updated:** [June 22, 2024, 2:25pm UTC](https://discourse.slicer.org/t/build-errors-with-slicer-error-lnk2005/36956 "2024-06-22T14:25:25Z")

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Dear friends, This issue has troubled me for a long time. I have upgraded to different versions of Slicer(5.6,main) and also switched between different versions of Visual Studio, but the problem persists. Does anyone ha…

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## [Convert nii.gz into DICOM series through python](https://discourse.slicer.org/t/convert-nii-gz-into-dicom-series-through-python/41675)

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**Author:** [@Shabina\_A](https://discourse.slicer.org/u/Shabina_A)\
**Replies:** 0\
**Last updated:** [February 13, 2025, 9:51am UTC](https://discourse.slicer.org/t/convert-nii-gz-into-dicom-series-through-python/41675 "2025-02-13T09:51:09Z")

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I did according to Create DICOM series using python But it is throwing in getNode raise MRMLNodeNotFoundException(“could not find nodes in the scene by name or id ‘%s’” % (pattern if (isinstance(pattern, str)) else “”)) …

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## [Skull / Skin of head segmentation rotation](https://discourse.slicer.org/t/skull-skin-of-head-segmentation-rotation/41607)

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**Author:** [@mxtt](https://discourse.slicer.org/u/mxtt)\
**Replies:** 5\
**Last updated:** [February 13, 2025, 9:10am UTC](https://discourse.slicer.org/t/skull-skin-of-head-segmentation-rotation/41607 "2025-02-13T09:10:39Z")

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So I have this segmentation of the skin of a head, I also have the skull (not displayed here). Does anyone have an intelligent way to rotate it so that is is positioned correctly - by correctly I essentially mean rota…

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## [Segmentation from reference segment](https://discourse.slicer.org/t/segmentation-from-reference-segment/41539)

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**Author:** [@slicerpy](https://discourse.slicer.org/u/slicerpy)\
**Replies:** 1\
**Last updated:** [February 12, 2025, 2:39pm UTC](https://discourse.slicer.org/t/segmentation-from-reference-segment/41539 "2025-02-12T14:39:34Z")

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Hello, I’m looking to automate a somewhat complex manual segmentation and trimming process. I would like to explore all the available options for this. Specifically, I’m wondering if Slicer has a feature to segment base…

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## [Register custom layout on Slicer start from custom module](https://discourse.slicer.org/t/register-custom-layout-on-slicer-start-from-custom-module/41618)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 3\
**Last updated:** [February 12, 2025, 12:19pm UTC](https://discourse.slicer.org/t/register-custom-layout-on-slicer-start-from-custom-module/41618 "2025-02-12T12:19:40Z")

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Hello, a module I have developed uses a few different custom layouts. Currently, these custom layouts are registered in the module widget’s setup() method. However, when users save a scene using one of these layouts, cl…

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## [Extract centerline via python](https://discourse.slicer.org/t/extract-centerline-via-python/41631)

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**Author:** [@laurabc](https://discourse.slicer.org/u/laurabc)\
**Replies:** 0\
**Last updated:** [February 11, 2025, 3:32pm UTC](https://discourse.slicer.org/t/extract-centerline-via-python/41631 "2025-02-11T15:32:35Z")

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I’ve come across several posts about this module, but I haven’t been able to get it working with a Python script. I want to extract the centerline of the aortic root and obtain orthogonal planes across the centerline for…

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## [Plans on european CE marking?](https://discourse.slicer.org/t/plans-on-european-ce-marking/41629)

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**Author:** [@FredrikM](https://discourse.slicer.org/u/FredrikM)\
**Replies:** 1\
**Last updated:** [February 11, 2025, 2:12pm UTC](https://discourse.slicer.org/t/plans-on-european-ce-marking/41629 "2025-02-11T14:12:45Z")

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Hi! 3D slicer is great! Are there any plans on getting european CE-marking?

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## [Animating Spheres (or markups) Using Sequencer](https://discourse.slicer.org/t/animating-spheres-or-markups-using-sequencer/41494)

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**Author:** [@mrsh0r3s](https://discourse.slicer.org/u/mrsh0r3s)\
**Replies:** 1\
**Last updated:** [February 10, 2025, 11:18pm UTC](https://discourse.slicer.org/t/animating-spheres-or-markups-using-sequencer/41494 "2025-02-10T23:18:59Z")

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Hello, I am trying to animate some markers in slicer. Basically, I want a bunch of spheres that change sizes and colors as time progresses. I did some digging and reached the conclusion that the parameters of markup con…

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## [How to programmatically set Terminology Name and Category for vtkMRMLSegmentationNode?](https://discourse.slicer.org/t/how-to-programmatically-set-terminology-name-and-category-for-vtkmrmlsegmentationnode/41504)

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**Author:** [@baderstine](https://discourse.slicer.org/u/baderstine)\
**Replies:** 2\
**Last updated:** [February 10, 2025, 5:13pm UTC](https://discourse.slicer.org/t/how-to-programmatically-set-terminology-name-and-category-for-vtkmrmlsegmentationnode/41504 "2025-02-10T17:13:17Z")

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Operating system: MacOS 15.3 Slicer version: 5.6.2 In my slicer extension, I am loading image and label (segmentation) volumes from a database. I have figured out how to load a custom terminology json file when the ex…

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## [3D image slicing using python](https://discourse.slicer.org/t/3d-image-slicing-using-python/41548)

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**Author:** [@Eko\_Pujiyulianto](https://discourse.slicer.org/u/Eko_Pujiyulianto)\
**Replies:** 1\
**Last updated:** [February 9, 2025, 7:31pm UTC](https://discourse.slicer.org/t/3d-image-slicing-using-python/41548 "2025-02-09T19:31:34Z")

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Hello, My name is Eko, I would like to discuss how to slice the 3D model using python and get the sliced plane. The illustration of slicing process is shown in the attached figure King regards Eko

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## [Detect closed polydata line](https://discourse.slicer.org/t/detect-closed-polydata-line/41553)

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**Author:** [@darabi](https://discourse.slicer.org/u/darabi)\
**Replies:** 1\
**Last updated:** [February 8, 2025, 2:28pm UTC](https://discourse.slicer.org/t/detect-closed-polydata-line/41553 "2025-02-08T14:28:44Z")

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Hello, I have a model which has a rim which is detectable with vtkFeatureEdges by using SetFeatureEdges(True) and SetFeatureAngle to a value between 35 and 45. Decreasing the feature angle incrementally and selecting t…

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## [Unable to install packages through the Python Console](https://discourse.slicer.org/t/unable-to-install-packages-through-the-python-console/41550)

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**Author:** [@dpvaldes](https://discourse.slicer.org/u/dpvaldes)\
**Replies:** 1\
**Last updated:** [February 7, 2025, 4:30pm UTC](https://discourse.slicer.org/t/unable-to-install-packages-through-the-python-console/41550 "2025-02-07T16:30:48Z")

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I’m trying to install the pandas package through the Python console in Slicer. I’m running Slicer 5.8 in macOS Sequoia 15.3 from slicer.util import pip\_install pip\_install(‘pandas’) shows me this output: error:…

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## [Message window at start](https://discourse.slicer.org/t/message-window-at-start/41555)

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**Author:** [@Djonathan\_Souza](https://discourse.slicer.org/u/Djonathan_Souza)\
**Replies:** 2\
**Last updated:** [February 7, 2025, 2:22pm UTC](https://discourse.slicer.org/t/message-window-at-start/41555 "2025-02-07T14:22:42Z")

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Hey,Hi, I’d like to remove the message that appears after the application starts. I’m developing, so I need it to don’t show to the user when it starts Thanks!

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## [Destroy qt.QPushButton](https://discourse.slicer.org/t/destroy-qt-qpushbutton/36210)

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**Author:** [@dfajtai](https://discourse.slicer.org/u/dfajtai)\
**Replies:** 5\
**Last updated:** [February 7, 2025, 1:34pm UTC](https://discourse.slicer.org/t/destroy-qt-qpushbutton/36210 "2025-02-07T13:34:51Z")

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I have successfully created a module based on the SimpleFilters module. It works fine if I have one “custom” filter. By this, I mean that there is only one element in the combo box. When I add more than one, I need to …

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## [Timeout waiting for kernel\_info reply from 605fe2fe-6d06-4d71-a2e1-001bf](https://discourse.slicer.org/t/timeout-waiting-for-kernel-info-reply-from-605fe2fe-6d06-4d71-a2e1-001bf/41551)

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**Author:** [@Saurabh\_Mishra](https://discourse.slicer.org/u/Saurabh_Mishra)\
**Replies:** 0\
**Last updated:** [February 7, 2025, 11:56am UTC](https://discourse.slicer.org/t/timeout-waiting-for-kernel-info-reply-from-605fe2fe-6d06-4d71-a2e1-001bf/41551 "2025-02-07T11:56:02Z")

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I am using one dockerfile to create one jupyterImage # Base image with Jupyter Notebook FROM jupyter/base-notebook # Set environment variables ENV DEBIAN\_FRONTEND=noninteractive ENV TZ=Etc/UTC ENV DISPLAY=:1 # Switch …

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## [Load image at Start](https://discourse.slicer.org/t/load-image-at-start/41526)

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**Author:** [@Djonathan\_Souza](https://discourse.slicer.org/u/Djonathan_Souza)\
**Replies:** 1\
**Last updated:** [February 6, 2025, 6:34pm UTC](https://discourse.slicer.org/t/load-image-at-start/41526 "2025-02-06T18:34:15Z")

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Hello! I need to start Slicer and load an image. If I delete everything after “study\_path,” the application loads the image, but I need these commands. “subprocess.call(\[”/opt/slicer/Slicer", “–no-splash”, “–fullscree…

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## [Build Slicer with SlicerRT](https://discourse.slicer.org/t/build-slicer-with-slicerrt/41445)

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**Author:** [@SSDad](https://discourse.slicer.org/u/SSDad)\
**Replies:** 5\
**Last updated:** [February 5, 2025, 11:45am UTC](https://discourse.slicer.org/t/build-slicer-with-slicerrt/41445 "2025-02-05T11:45:36Z")

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I am trying to follow this website to add SlicerRT Extension to Slicer I have a couple questions here. What does the following sentence mean? " \* When configuring the project set the Slicer\_DIR to the Slicer versio…

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## [Please help with installing Pandas into Slicer Python](https://discourse.slicer.org/t/please-help-with-installing-pandas-into-slicer-python/41402)

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**Author:** [@Misterkim](https://discourse.slicer.org/u/Misterkim)\
**Replies:** 2\
**Last updated:** [February 4, 2025, 9:04pm UTC](https://discourse.slicer.org/t/please-help-with-installing-pandas-into-slicer-python/41402 "2025-02-04T21:04:01Z")

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I ran the following from the PythonSlicer console: from slicer.util import pip\_install pip\_install("pandas\>2") and received the following error: Traceback (most recent call last): File "\<console\>", line 1, in \<module\>…

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## [Hide Extensions from toolbar](https://discourse.slicer.org/t/hide-extensions-from-toolbar/41471)

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**Author:** [@Djonathan\_Souza](https://discourse.slicer.org/u/Djonathan_Souza)\
**Replies:** 7\
**Last updated:** [February 4, 2025, 8:18pm UTC](https://discourse.slicer.org/t/hide-extensions-from-toolbar/41471 "2025-02-04T20:18:08Z")

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Hi, How can I hide toolbar extensions? Or just remove it. I need to remove the python icon from there

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## [Loading scene as slicer start](https://discourse.slicer.org/t/loading-scene-as-slicer-start/41488)

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**Author:** [@Djonathan\_Souza](https://discourse.slicer.org/u/Djonathan_Souza)\
**Replies:** 2\
**Last updated:** [February 4, 2025, 1:12pm UTC](https://discourse.slicer.org/t/loading-scene-as-slicer-start/41488 "2025-02-04T13:12:11Z")

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how to load an image as soon as it starts. I just do it but when i use “–python-script” he just ignore the path to load

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## [How to Implement Marker-Based Tracking and 3D Visualization in 3D Slicer (Similar to Video Example)](https://discourse.slicer.org/t/how-to-implement-marker-based-tracking-and-3d-visualization-in-3d-slicer-similar-to-video-example/41473)

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**Author:** [@Navneet](https://discourse.slicer.org/u/Navneet)\
**Replies:** 0\
**Last updated:** [February 3, 2025, 9:05pm UTC](https://discourse.slicer.org/t/how-to-implement-marker-based-tracking-and-3d-visualization-in-3d-slicer-similar-to-video-example/41473 "2025-02-03T21:05:19Z")

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Hello 3D Slicer Community, I am looking to replicate a system similar to the one demonstrated in this video: Marker-Based Tracking and Visualization in 3D Slicer. The system involves: Using a physical marker (e.g., fi…

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## [Slicer does not accept certain transform values](https://discourse.slicer.org/t/slicer-does-not-accept-certain-transform-values/41398)

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**Author:** [@TheZappie](https://discourse.slicer.org/u/TheZappie)\
**Replies:** 1\
**Last updated:** [February 3, 2025, 8:24am UTC](https://discourse.slicer.org/t/slicer-does-not-accept-certain-transform-values/41398 "2025-02-03T08:24:37Z")

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3d slicer does not import volumes that I create with the python code below. What constraint in 3D slicer is causing this? import numpy as np import nibabel as nib from nibabel import affines data = np.random.normal(s…

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## [Proposal for dental segmentator](https://discourse.slicer.org/t/proposal-for-dental-segmentator/41369)

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**Author:** [@Esteban\_Barreiro](https://discourse.slicer.org/u/Esteban_Barreiro)\
**Replies:** 2\
**Last updated:** [January 31, 2025, 9:47pm UTC](https://discourse.slicer.org/t/proposal-for-dental-segmentator/41369 "2025-01-31T21:47:29Z")

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Hi everyone! Im here to ask if is possible to: change opacity for the segments in DentalSegmentator Extension (whithout having to re paint them in the SegmenEditor) Cancel editing by pressing ESC By the way, I …

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## [Building Slicer from /opt directory reports "permission denied" error](https://discourse.slicer.org/t/building-slicer-from-opt-directory-reports-permission-denied-error/41352)

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**Author:** [@ferhue](https://discourse.slicer.org/u/ferhue)\
**Replies:** 5\
**Last updated:** [January 29, 2025, 1:40pm UTC](https://discourse.slicer.org/t/building-slicer-from-opt-directory-reports-permission-denied-error/41352 "2025-01-29T13:40:41Z")

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I am getting an error when compiling Slicer on Ubu22.04 (from git master, cloned on Jan24) but it is a bit cryptic. Could you let me know what could be happening? After 3 hours of building, it ends with: -- Setting CPA…

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