# Support

**URL:** https://discourse.slicer.org/c/support/11.md?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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## [Manually Adjusting Transform - Applied Object Seems to Jump Around; Matrixes Not Edited As Expected ](https://discourse.slicer.org/t/manually-adjusting-transform-applied-object-seems-to-jump-around-matrixes-not-edited-as-expected/34086)

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**Author:** [@tpal\_1](https://discourse.slicer.org/u/tpal_1)\
**Replies:** 21\
**Last updated:** [February 5, 2024, 5:18pm UTC](https://discourse.slicer.org/t/manually-adjusting-transform-applied-object-seems-to-jump-around-matrixes-not-edited-as-expected/34086 "2024-02-05T17:18:29Z")

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Operating system: Mac OS Monterey 12.7.1 Slicer version: 5.6.1 (and 5.2.2) I have had consistent issues when manually adjusting transforms in Slicer 5.2.2 and Slicer 5.6.1. It seems that minor changes result in the tra…

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## [Convert planar contour to ribbon model in code](https://discourse.slicer.org/t/convert-planar-contour-to-ribbon-model-in-code/34119)

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**Author:** [@susk](https://discourse.slicer.org/u/susk)\
**Replies:** 1\
**Last updated:** [February 5, 2024, 11:17am UTC](https://discourse.slicer.org/t/convert-planar-contour-to-ribbon-model-in-code/34119 "2024-02-05T11:17:18Z")

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Hi there, I have loaded a segmentation into 3D slicer as a planar contour, and am able to convert these planar contours into a Ribbon model representation manually in the segmentations module, by pressing ‘create’ for t…

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## [ultrasound segmentation](https://discourse.slicer.org/t/ultrasound-segmentation/34146)

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**Author:** [@roxana](https://discourse.slicer.org/u/roxana)\
**Replies:** 1\
**Last updated:** [February 4, 2024, 7:43pm UTC](https://discourse.slicer.org/t/ultrasound-segmentation/34146 "2024-02-04T19:43:43Z")

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Hello, Is it possible to extract radiomic data from ultrasound images? I uploaded and segmented a ROI, but it is not a volume, so that I can not extract features. Is there any other way? Or I should use another soft? Th…

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## [Best way to extract/isolate areas from a segment ? ](https://discourse.slicer.org/t/best-way-to-extract-isolate-areas-from-a-segment/34125)

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**Author:** [@dcg494](https://discourse.slicer.org/u/dcg494)\
**Replies:** 3\
**Last updated:** [February 4, 2024, 7:24pm UTC](https://discourse.slicer.org/t/best-way-to-extract-isolate-areas-from-a-segment/34125 "2024-02-04T19:24:42Z")

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Hi all, i’m looking for help getting parts of this segment isolated. As you can see in the picture, the green area is the segment and i’m trying to isolate the airways from the area outside of the head. Very new to 3-d …

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## [High resolution 3D model from CT scans from multiple planes?](https://discourse.slicer.org/t/high-resolution-3d-model-from-ct-scans-from-multiple-planes/34112)

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**Author:** [@jakezw](https://discourse.slicer.org/u/jakezw)\
**Replies:** 4\
**Last updated:** [February 4, 2024, 4:13pm UTC](https://discourse.slicer.org/t/high-resolution-3d-model-from-ct-scans-from-multiple-planes/34112 "2024-02-04T16:13:42Z")

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hi, I have dicom data in the three major planes (axial coronal sagittal) I can load all 3 into the 3D reconstruction viewer and it displays fantastic, with high level detail of the scanned head. I wish to export this a…

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## [Import CSO segmentation into Slicer](https://discourse.slicer.org/t/import-cso-segmentation-into-slicer/22601)

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**Author:** [@Fabio\_Nunes](https://discourse.slicer.org/u/Fabio_Nunes)\
**Replies:** 5\
**Last updated:** [February 4, 2024, 3:04pm UTC](https://discourse.slicer.org/t/import-cso-segmentation-into-slicer/22601 "2024-02-04T15:04:57Z")

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Dear 3D Slicer team, I’m working with CSO files (contour segmentation objects) that have been extracted from other programs. In my case, the CSO files represent the segmentation of the pericardium. I’ve tried the sugges…

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## [3D slicer python console](https://discourse.slicer.org/t/3d-slicer-python-console/34133)

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**Author:** [@sefika](https://discourse.slicer.org/u/sefika)\
**Replies:** 0\
**Last updated:** [February 3, 2024, 9:56am UTC](https://discourse.slicer.org/t/3d-slicer-python-console/34133 "2024-02-03T09:56:07Z")

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Can I convert the color to grayscale with code on the 3D slicer Python console?

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## [How to show/hide ruller in 3DView by code?](https://discourse.slicer.org/t/how-to-show-hide-ruller-in-3dview-by-code/34132)

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**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\
**Replies:** 0\
**Last updated:** [February 3, 2024, 9:51am UTC](https://discourse.slicer.org/t/how-to-show-hide-ruller-in-3dview-by-code/34132 "2024-02-03T09:51:49Z")

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Hi everyone! I need to manage ruller visibility in my module and I can´t find it in forum or script repository. Api search gives me to vtkMRMLAbstractViewNode but I just find GetRulerEnabled but not SetRulerEnabled… T…

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## [Fail to install \`scikit-image\` - update pip version in Slicer](https://discourse.slicer.org/t/fail-to-install-scikit-image-update-pip-version-in-slicer/23343)

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**Author:** [@S\_Arbabi](https://discourse.slicer.org/u/S_Arbabi)\
**Replies:** 2\
**Last updated:** [February 3, 2024, 12:28am UTC](https://discourse.slicer.org/t/fail-to-install-scikit-image-update-pip-version-in-slicer/23343 "2024-02-03T00:28:18Z")

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I wanted to install scikit-image library using pip\_install(“scikit-image”), when I got the warning: WARNING: You are using pip version 21.1.2; however, version 21.3.1 is available. You should consider upgrading via the …

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## [Importing unstructured point cloud data from filesystem](https://discourse.slicer.org/t/importing-unstructured-point-cloud-data-from-filesystem/34126)

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**Author:** [@a.tamaz](https://discourse.slicer.org/u/a.tamaz)\
**Replies:** 0\
**Last updated:** [February 2, 2024, 7:49pm UTC](https://discourse.slicer.org/t/importing-unstructured-point-cloud-data-from-filesystem/34126 "2024-02-02T19:49:06Z")

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Hi, is it possible to import unstructured point cloud data in the Slicer UI? Ideally using .ply format. I have tried the following .ply and .vtk files – Slicer loads both as “Model” and shows “Number of points” as 5 in…

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## [Get 3d model segmentations for 2d tracked images](https://discourse.slicer.org/t/get-3d-model-segmentations-for-2d-tracked-images/33916)

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**Author:** [@pfrwilson](https://discourse.slicer.org/u/pfrwilson)\
**Replies:** 2\
**Last updated:** [February 2, 2024, 6:48pm UTC](https://discourse.slicer.org/t/get-3d-model-segmentations-for-2d-tracked-images/33916 "2024-02-02T18:48:46Z")

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I am using slicer to display tracked 2d ultrasound images of the prostate. My data consists of sequence browser nodes controlling the 2D image data and tracking transformation. By creating a 3d volume reconstruction, se…

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## [Cross section analysis in VMTK module](https://discourse.slicer.org/t/cross-section-analysis-in-vmtk-module/34097)

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**Author:** [@michaelli](https://discourse.slicer.org/u/michaelli)\
**Replies:** 7\
**Last updated:** [February 2, 2024, 1:40pm UTC](https://discourse.slicer.org/t/cross-section-analysis-in-vmtk-module/34097 "2024-02-02T13:40:11Z")

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I can convert a cross section and convert to a segmentation and then convert it back to a model; then go to the next cross section by browsing in the cross sectional analysis module. Finally, I can save them to STL. T…

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## [Troubles with cardiac MRI](https://discourse.slicer.org/t/troubles-with-cardiac-mri/34113)

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**Author:** [@Lu\_17](https://discourse.slicer.org/u/Lu_17)\
**Replies:** 0\
**Last updated:** [February 2, 2024, 10:45am UTC](https://discourse.slicer.org/t/troubles-with-cardiac-mri/34113 "2024-02-02T10:45:41Z")

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Operating system: Windows 10 Slicer version: 5.6.1 Hello, I\`m new to 3d Slicer and currently having trouble with a cardic mri. After importing the dicom files some volume sequences appear only through thin stripes as i…

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## [N4ITK module on 3D slicer](https://discourse.slicer.org/t/n4itk-module-on-3d-slicer/34111)

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**Author:** [@e0032127](https://discourse.slicer.org/u/e0032127)\
**Replies:** 0\
**Last updated:** [February 2, 2024, 10:45am UTC](https://discourse.slicer.org/t/n4itk-module-on-3d-slicer/34111 "2024-02-02T10:45:23Z")

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Hi everyone! Has anyone had any issues regarding FSL FAST segmentation pipeline; whereby the subcortical (eg thalamus) gets segmented into white matter tissue? I’ve tried to solve this problem by using the N4ITK bias fi…

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## [Convert .tck to .vtk streamlines](https://discourse.slicer.org/t/convert-tck-to-vtk-streamlines/32870)

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**Author:** [@yi\_yang](https://discourse.slicer.org/u/yi_yang)\
**Replies:** 3\
**Last updated:** [February 2, 2024, 10:32am UTC](https://discourse.slicer.org/t/convert-tck-to-vtk-streamlines/32870 "2024-02-02T10:32:11Z")

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Hi, I am trying to convert some tractography data from .tck to .vtk format. But I can’t get the correct results that match the image loaded in slicer. I’m not very familiar to vtk files and slicer so I’m seeking for he…

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## [Is it possible to change to Dark Mode Style by code?](https://discourse.slicer.org/t/is-it-possible-to-change-to-dark-mode-style-by-code/34093)

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**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\
**Replies:** 3\
**Last updated:** [February 2, 2024, 7:23am UTC](https://discourse.slicer.org/t/is-it-possible-to-change-to-dark-mode-style-by-code/34093 "2024-02-02T07:23:08Z")

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I want to put my SlicerCustomApp in Dark Mode by default. I´m looking for it in the forum and in API but I can´t get it… What is the CmakeList parameter to add? Should be possible to add it to a module instead? Thanks…

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## [3D Model of membranous labyrinth from serial histological sections](https://discourse.slicer.org/t/3d-model-of-membranous-labyrinth-from-serial-histological-sections/34088)

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**Author:** [@Zbynek](https://discourse.slicer.org/u/Zbynek)\
**Replies:** 1\
**Last updated:** [February 2, 2024, 4:30am UTC](https://discourse.slicer.org/t/3d-model-of-membranous-labyrinth-from-serial-histological-sections/34088 "2024-02-02T04:30:06Z")

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Operating system: Windows 1.2309.12711.0 Slicer version: 3D Slicer 5.6.1 Expected behavior: Actual behavior: Can anyone tell me if 3D Slicer is suitable for building a 3D model of the membranous labyrinth from serial…

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## [Python Debugger Issue](https://discourse.slicer.org/t/python-debugger-issue/34098)

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**Author:** [@ogdenk](https://discourse.slicer.org/u/ogdenk)\
**Replies:** 0\
**Last updated:** [February 1, 2024, 9:13pm UTC](https://discourse.slicer.org/t/python-debugger-issue/34098 "2024-02-01T21:13:06Z")

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I have an issue with trying to use the python debugger module. I have connected it to Pycharm, that was very easy and the connection seems to be ok. However, once I make the connection, I can’t get any code to run in P…

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## [Python Script to check if the 3D Slicer is in dark or light mode?](https://discourse.slicer.org/t/python-script-to-check-if-the-3d-slicer-is-in-dark-or-light-mode/34096)

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**Author:** [@nicholas489](https://discourse.slicer.org/u/nicholas489)\
**Replies:** 0\
**Last updated:** [February 1, 2024, 5:35pm UTC](https://discourse.slicer.org/t/python-script-to-check-if-the-3d-slicer-is-in-dark-or-light-mode/34096 "2024-02-01T17:35:57Z")

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Hi, I’m trying to write some code to check if the user’s 3D Slicer application is in either dark or light mode. I’m looking for it in the forum and inside the API docs but I can’t seem to find anything. Thanks in advance…

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## [Is Nifti (converted from raw DICOM) accurate for segmentation?](https://discourse.slicer.org/t/is-nifti-converted-from-raw-dicom-accurate-for-segmentation/34092)

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**Author:** [@benalb](https://discourse.slicer.org/u/benalb)\
**Replies:** 0\
**Last updated:** [February 1, 2024, 1:05pm UTC](https://discourse.slicer.org/t/is-nifti-converted-from-raw-dicom-accurate-for-segmentation/34092 "2024-02-01T13:05:14Z")

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There seems to be a lot of correction performed during the dicom to nifti conversion, such as converting to equal slice thickness and correcting for gantry tilt. If I perform segmentation on raw DICOMs loaded into Slice…

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## [bronchoscopy option is not available? what to do?](https://discourse.slicer.org/t/bronchoscopy-option-is-not-available-what-to-do/34089)

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**Author:** [@MONICA\_R](https://discourse.slicer.org/u/MONICA_R)\
**Replies:** 0\
**Last updated:** [February 1, 2024, 12:03pm UTC](https://discourse.slicer.org/t/bronchoscopy-option-is-not-available-what-to-do/34089 "2024-02-01T12:03:56Z")

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Operating system:windows Slicer version:4.3.0 Expected behavior: Actual behavior:

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## [Export segment threshold](https://discourse.slicer.org/t/export-segment-threshold/34083)

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**Author:** [@juedcrt](https://discourse.slicer.org/u/juedcrt)\
**Replies:** 0\
**Last updated:** [February 1, 2024, 12:03pm UTC](https://discourse.slicer.org/t/export-segment-threshold/34083 "2024-02-01T12:03:45Z")

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Operating system: Windows Slicer version: 5.4.0 Expected behavior: Actual behavior: Hello I am trying to manually segment brain lesions. I find that the threshold tool helps me to delineate these lesions but once I…

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## [Adjusting Segment Threshold](https://discourse.slicer.org/t/adjusting-segment-threshold/34052)

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**Author:** [@jamieawren](https://discourse.slicer.org/u/jamieawren)\
**Replies:** 6\
**Last updated:** [February 1, 2024, 8:43am UTC](https://discourse.slicer.org/t/adjusting-segment-threshold/34052 "2024-02-01T08:43:38Z")

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Hi Everyone, I set a minimum threshold of 200 to use as a mask to create segments on CT data. I’ve realized that 200 was too high for my data, and I would like to readjust the threshold downward. Is there a way to do th…

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## [Radius Extraction from centerline](https://discourse.slicer.org/t/radius-extraction-from-centerline/34066)

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**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 4\
**Last updated:** [January 31, 2024, 3:10pm UTC](https://discourse.slicer.org/t/radius-extraction-from-centerline/34066 "2024-01-31T15:10:52Z")

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Hi to everyone. I’m working with centerlines, which I made with a external python code. From this code I return the centerlines as Markups nodes, and now I would like to extract radius info. For this purpose I use the C…

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## [Problem with AutoSave module](https://discourse.slicer.org/t/problem-with-autosave-module/34046)

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**Author:** [@MJamal](https://discourse.slicer.org/u/MJamal)\
**Replies:** 7\
**Last updated:** [January 31, 2024, 12:45pm UTC](https://discourse.slicer.org/t/problem-with-autosave-module/34046 "2024-01-31T12:45:33Z")

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Hello, How can I prevent the Slicer main window from becoming unresponsive when using the autosave feature? I’ve observed significant lag in the main window after enabling autosave. Is it running on the same thread as S…

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## [Slicer 5.6 not starting with custom extension](https://discourse.slicer.org/t/slicer-5-6-not-starting-with-custom-extension/33439)

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**Author:** [@Vincebisca](https://discourse.slicer.org/u/Vincebisca)\
**Replies:** 12\
**Last updated:** [January 31, 2024, 9:37am UTC](https://discourse.slicer.org/t/slicer-5-6-not-starting-with-custom-extension/33439 "2024-01-31T09:37:00Z")

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Hello, A year ago I developped a custom extension as part of an internal project on 3D Slicer 4.11. At the time, I managed to transfer to Slicer 5.0 without issues and use the extension on this version too. The project…

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## [Customize keyboard shortcuts in Slicer?](https://discourse.slicer.org/t/customize-keyboard-shortcuts-in-slicer/32891)

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**Author:** [@mvergnat](https://discourse.slicer.org/u/mvergnat)\
**Replies:** 2\
**Last updated:** [January 31, 2024, 8:41am UTC](https://discourse.slicer.org/t/customize-keyboard-shortcuts-in-slicer/32891 "2024-01-31T08:41:32Z")

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Hello! dear all, I would like to change few keyboard shortcuts: I work on an echo loop and I am doing somme segmentation. to well identify structures, I often need to navigate quickly in the frames. the normal schor…

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## [Given plane center and normal, How to calculate baseToNode](https://discourse.slicer.org/t/given-plane-center-and-normal-how-to-calculate-basetonode/34055)

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**Author:** [@angolin22\_fan](https://discourse.slicer.org/u/angolin22_fan)\
**Replies:** 0\
**Last updated:** [January 31, 2024, 7:55am UTC](https://discourse.slicer.org/t/given-plane-center-and-normal-how-to-calculate-basetonode/34055 "2024-01-31T07:55:03Z")

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Dear teacher, Hello, Thanks for your excellent work! I have a question, If I know the plane center(c1,c2,c3) and normal(n1,n2,n3), How can I calculate the ‘baseToNode’?

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## [IXI data set for tractography](https://discourse.slicer.org/t/ixi-data-set-for-tractography/34054)

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**Author:** [@Pranali](https://discourse.slicer.org/u/Pranali)\
**Replies:** 0\
**Last updated:** [January 31, 2024, 7:19am UTC](https://discourse.slicer.org/t/ixi-data-set-for-tractography/34054 "2024-01-31T07:19:01Z")

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has anyone worked with IXI DTI data? I have been facing issue while converting it to .nhrd.

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## [3D Slicer Mauritania](https://discourse.slicer.org/t/3d-slicer-mauritania/34043)

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**Author:** [@Mohamedou\_Fi](https://discourse.slicer.org/u/Mohamedou_Fi)\
**Replies:** 3\
**Last updated:** [January 30, 2024, 11:06pm UTC](https://discourse.slicer.org/t/3d-slicer-mauritania/34043 "2024-01-30T23:06:03Z")

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Hello everyone, and thank you for welcoming us today. In 40 project week. We are the Mauritania Team, beginners in the 3D Slicer community, with a strong desire to contribute to medical image fields. Our project focus…

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