# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=84

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

**Page:** 85

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## [Draw principal axes](https://discourse.slicer.org/t/draw-principal-axes/27144)

<div class="topic-metadata">

**Author:** [@soukup.la](https://discourse.slicer.org/u/soukup.la)\
**Replies:** 4\
**Last updated:** [July 11, 2024, 4:44am UTC](https://discourse.slicer.org/t/draw-principal-axes/27144 "2024-07-11T04:44:42Z")

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Hello, I would like to draw Principal axes (segment statistic) using Python console. Is it possible please? thank you!

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## [Inquiry about the 'Auto' Control Mode in qMRMLVolumeThresholdWidget](https://discourse.slicer.org/t/inquiry-about-the-auto-control-mode-in-qmrmlvolumethresholdwidget/37232)

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**Author:** [@WilliamDaniel](https://discourse.slicer.org/u/WilliamDaniel)\
**Replies:** 1\
**Last updated:** [July 11, 2024, 4:36am UTC](https://discourse.slicer.org/t/inquiry-about-the-auto-control-mode-in-qmrmlvolumethresholdwidget/37232 "2024-07-11T04:36:37Z")

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Dear 3D Slicer Community, I am a learner of Slicer module development. I am writing to inquire about the underlying principle/algorithm behind the “Auto” option in the Control Mode of the qMRMLVolumeThresholdWidget. …

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## [Convert Monai bundle to torch file for SlicerMONAIAuto3DSeg](https://discourse.slicer.org/t/convert-monai-bundle-to-torch-file-for-slicermonaiauto3dseg/34836)

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**Author:** [@slava](https://discourse.slicer.org/u/slava)\
**Replies:** 9\
**Last updated:** [July 10, 2024, 9:44pm UTC](https://discourse.slicer.org/t/convert-monai-bundle-to-torch-file-for-slicermonaiauto3dseg/34836 "2024-07-10T21:44:32Z")

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Hi, I am trying to use my network trained using Monai Auto3Dseg in the SlicerMONAIAuto3DSeg plugin. SlicerMONAIAuto3DSeg imports the torch file with a list including config information and the network weights. Monai out…

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## [Intersect segments stored in two different segmentations](https://discourse.slicer.org/t/intersect-segments-stored-in-two-different-segmentations/37305)

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**Author:** [@Noa](https://discourse.slicer.org/u/Noa)\
**Replies:** 5\
**Last updated:** [July 10, 2024, 7:31pm UTC](https://discourse.slicer.org/t/intersect-segments-stored-in-two-different-segmentations/37305 "2024-07-10T19:31:09Z")

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Hello, I try to intersect two segmentations : tumor1 and tumor2, segmented from volume1 and volume2. I created a transform, 2to1, to overlay segment 2 on segment 1. How do I intersect these two segmentations? Thank you …

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## [Issue converting NRRD file to PLY file](https://discourse.slicer.org/t/issue-converting-nrrd-file-to-ply-file/37128)

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**Author:** [@mtyack](https://discourse.slicer.org/u/mtyack)\
**Replies:** 11\
**Last updated:** [July 10, 2024, 6:56pm UTC](https://discourse.slicer.org/t/issue-converting-nrrd-file-to-ply-file/37128 "2024-07-10T18:56:58Z")

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Hello, I am having a new issue when converting and opening saved files and hoping for some troubleshooting advice. In the past, I have segmented out heads and jaws within one large file, and saved them individually fro…

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## [Compare PCA components](https://discourse.slicer.org/t/compare-pca-components/37300)

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**Author:** [@Dani98](https://discourse.slicer.org/u/Dani98)\
**Replies:** 1\
**Last updated:** [July 10, 2024, 5:03pm UTC](https://discourse.slicer.org/t/compare-pca-components/37300 "2024-07-10T17:03:17Z")

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I’m doing a PCA analysis and I’m using 5 PC components For each component I make 2 variations: +100 and -100 At the end of the work I’d like to visualize the main directions of variations with respect to the mean shape…

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## [Wrap\_python build error in qt loadable widget](https://discourse.slicer.org/t/wrap-python-build-error-in-qt-loadable-widget/37298)

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**Author:** [@fqzhice](https://discourse.slicer.org/u/fqzhice)\
**Replies:** 0\
**Last updated:** [July 10, 2024, 8:21am UTC](https://discourse.slicer.org/t/wrap-python-build-error-in-qt-loadable-widget/37298 "2024-07-10T08:21:31Z")

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Hi, In custom qt loadable extension, I set "WRAP\_PYTHON" and include "ctkDICOMDisplayedFieldGeneratorRuleFactory". I found this class is singleton and generate wrapper itself private: ... friend class PythonQtWrapp…

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## [Scenes library / database](https://discourse.slicer.org/t/scenes-library-database/37293)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 2\
**Last updated:** [July 10, 2024, 12:41am UTC](https://discourse.slicer.org/t/scenes-library-database/37293 "2024-07-10T00:41:53Z")

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it would be great if we have scenes library similar to dicom library

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## [Saved files naming options](https://discourse.slicer.org/t/saved-files-naming-options/37294)

<div class="topic-metadata">

**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 0\
**Last updated:** [July 9, 2024, 7:12pm UTC](https://discourse.slicer.org/t/saved-files-naming-options/37294 "2024-07-09T19:12:18Z")

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great option if we are able to set default saved file naming option like date\_patient name \_mr etc

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## [Extensions index is down?](https://discourse.slicer.org/t/extensions-index-is-down/37290)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 1\
**Last updated:** [July 9, 2024, 6:45pm UTC](https://discourse.slicer.org/t/extensions-index-is-down/37290 "2024-07-09T18:45:41Z")

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For example, this does not work: https://slicer-packages.kitware.com/api/v1/app/5f4474d0e1d8c75dfc705482/extension And entering on the extensions manager I see this: \[Qt\] An OpenGL Core Profile was requested, but i…

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## [Weird results with dental segmentator](https://discourse.slicer.org/t/weird-results-with-dental-segmentator/37009)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 5\
**Last updated:** [July 9, 2024, 6:10pm UTC](https://discourse.slicer.org/t/weird-results-with-dental-segmentator/37009 "2024-07-09T18:10:32Z")

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@Thibault\_Pelletier weird results with dental segmentator , i had it outside ct and looks awkward

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## [Batch Processing Stl files into binary images for Radiomics](https://discourse.slicer.org/t/batch-processing-stl-files-into-binary-images-for-radiomics/37285)

<div class="topic-metadata">

**Author:** [@Steven\_A](https://discourse.slicer.org/u/Steven_A)\
**Replies:** 3\
**Last updated:** [July 9, 2024, 3:53pm UTC](https://discourse.slicer.org/t/batch-processing-stl-files-into-binary-images-for-radiomics/37285 "2024-07-09T15:53:04Z")

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Hi, is there a way to batch process the discretization of stl files into binary images to be loaded into either slicerradiomics or into pyradiomics for feature extraction? Or maybe there is a way to simply load in the st…

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## [No ID meta data (patient name etc) in dicom data - 3d slicer wont load data](https://discourse.slicer.org/t/no-id-meta-data-patient-name-etc-in-dicom-data-3d-slicer-wont-load-data/37283)

<div class="topic-metadata">

**Author:** [@Willa\_Coultley](https://discourse.slicer.org/u/Willa_Coultley)\
**Replies:** 1\
**Last updated:** [July 9, 2024, 3:20pm UTC](https://discourse.slicer.org/t/no-id-meta-data-patient-name-etc-in-dicom-data-3d-slicer-wont-load-data/37283 "2024-07-09T15:20:20Z")

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Hi all, first off: my data is not clinical (i.e., no patient information/sensitive data). I am analyzing a bird skull that is housed in a fair amount of limestone. second off: i am very, very new to 3d slicer and uct a…

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## [Can't add measurements to the closed curve](https://discourse.slicer.org/t/cant-add-measurements-to-the-closed-curve/37286)

<div class="topic-metadata">

**Author:** [@Miguel\_Nobre\_Menezes](https://discourse.slicer.org/u/Miguel_Nobre_Menezes)\
**Replies:** 0\
**Last updated:** [July 9, 2024, 3:09pm UTC](https://discourse.slicer.org/t/cant-add-measurements-to-the-closed-curve/37286 "2024-07-09T15:09:45Z")

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I’m trying to add measurements to the closed curve markup: \> # Create a new measurement instance \> \> last\_one = slicer.vtkMRMLMeasurementLength() \> \> # Configure the new measurement \> \> last\_one.SetName("last\_one") \> …

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## [When using Memos, the volume only has none. ](https://discourse.slicer.org/t/when-using-memos-the-volume-only-has-none/37280)

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**Author:** [@Wenjun\_Dong](https://discourse.slicer.org/u/Wenjun_Dong)\
**Replies:** 1\
**Last updated:** [July 9, 2024, 2:42pm UTC](https://discourse.slicer.org/t/when-using-memos-the-volume-only-has-none/37280 "2024-07-09T14:42:56Z")

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When I tried to use Memos, it showed None for volume in single volume. How can I do?

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## [Extension can't be installed!](https://discourse.slicer.org/t/extension-cant-be-installed/12012)

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**Author:** [@sunshine\_boycn](https://discourse.slicer.org/u/sunshine_boycn)\
**Replies:** 7\
**Last updated:** [July 9, 2024, 12:14pm UTC](https://discourse.slicer.org/t/extension-cant-be-installed/12012 "2024-07-09T12:14:51Z")

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Recently, Slicer can’t download the extension from extension manager. The hint is : No extensions found for win:64-bit, revision: ‘1c531bd’. Please try a different combination And my slicer is built on windows with th…

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## [Vmtk Network algorithm error for the big diameter change part](https://discourse.slicer.org/t/vmtk-network-algorithm-error-for-the-big-diameter-change-part/37253)

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**Author:** [@gang\_fang](https://discourse.slicer.org/u/gang_fang)\
**Replies:** 3\
**Last updated:** [July 9, 2024, 5:25am UTC](https://discourse.slicer.org/t/vmtk-network-algorithm-error-for-the-big-diameter-change-part/37253 "2024-07-09T05:25:25Z")

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Dear , all and developers I use the network extraction for the vessel model with big aneursym , but the network line go outside of the surface , seem not right. Is there solution for this situation?

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## [Slow smoothing process, CPU bound](https://discourse.slicer.org/t/slow-smoothing-process-cpu-bound/37266)

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**Author:** [@Mark\_Ryan](https://discourse.slicer.org/u/Mark_Ryan)\
**Replies:** 1\
**Last updated:** [July 9, 2024, 2:17am UTC](https://discourse.slicer.org/t/slow-smoothing-process-cpu-bound/37266 "2024-07-09T02:17:23Z")

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Have a 46 slice chest CT that I’ve upsampled to 196 slices using “crop volume” tool. Have performed segmentation on this using Totalsegmentator tool. Main issues are that the “apply to visible segments” checkbox in the …

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## [Combine Multiple Orientations / Volumes in Axial View](https://discourse.slicer.org/t/combine-multiple-orientations-volumes-in-axial-view/37073)

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**Author:** [@waterbottle](https://discourse.slicer.org/u/waterbottle)\
**Replies:** 1\
**Last updated:** [July 8, 2024, 4:33pm UTC](https://discourse.slicer.org/t/combine-multiple-orientations-volumes-in-axial-view/37073 "2024-07-08T16:33:50Z")

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Hi all, Still new to slicer. I am working on MRIs in Slicer. Some MRIs load in as one big volume which works for my needs, however others come split into “imageOrientationPatient X” where X = some number, typically from…

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## [MALPACA on several species - issue?](https://discourse.slicer.org/t/malpaca-on-several-species-issue/37139)

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**Author:** [@MSAC](https://discourse.slicer.org/u/MSAC)\
**Replies:** 11\
**Last updated:** [July 8, 2024, 3:44pm UTC](https://discourse.slicer.org/t/malpaca-on-several-species-issue/37139 "2024-07-08T15:44:38Z")

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Operating system: IOS Slicer version: 5.6.2 Hello Community! I am new to slicer and ALPACA and I would like to apply a Multi-template (MALPACA) to my data for GMM analysis. Some context: I am working with 4 modern sp…

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## [Visualization with Glyph Side mode](https://discourse.slicer.org/t/visualization-with-glyph-side-mode/36990)

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**Author:** [@capucinelab](https://discourse.slicer.org/u/capucinelab)\
**Replies:** 7\
**Last updated:** [July 8, 2024, 3:18pm UTC](https://discourse.slicer.org/t/visualization-with-glyph-side-mode/36990 "2024-07-08T15:18:43Z")

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Hello, I would like to have more details about the use of the color map visualization with the Glyph Side mode, on human skull scans. Is there a way to reduce the number of arrows, and choose to have them localized only…

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## [Is MONAI Auto3DSeg Whole body segmentation model based on SegResNet?](https://discourse.slicer.org/t/is-monai-auto3dseg-whole-body-segmentation-model-based-on-segresnet/37255)

<div class="topic-metadata">

**Author:** [@samuelholly](https://discourse.slicer.org/u/samuelholly)\
**Replies:** 1\
**Last updated:** [June 17, 2024, 10:01am UTC](https://discourse.slicer.org/t/is-monai-auto3dseg-whole-body-segmentation-model-based-on-segresnet/37255 "2024-06-17T10:01:47Z")

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Dear all, just a quick question: is the Whole body segmentation TS1 (v1.0.0) model based on the SegResNet architecture? Is there a paper describing this model? Thank you in advance. Best regards Samuel

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## [Are there automatic segmentation models for musculoskeletal anatomy?](https://discourse.slicer.org/t/are-there-automatic-segmentation-models-for-musculoskeletal-anatomy/37254)

<div class="topic-metadata">

**Author:** [@Roshawnbrown](https://discourse.slicer.org/u/Roshawnbrown)\
**Replies:** 4\
**Last updated:** [July 5, 2024, 1:14pm UTC](https://discourse.slicer.org/t/are-there-automatic-segmentation-models-for-musculoskeletal-anatomy/37254 "2024-07-05T13:14:34Z")

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Hello all, Thank you introducing this. Are there any segmentations available for musculoskeletal anatomy? Specifically, I am looking for joints, tendons, ligaments, bursae, and cartilage.If not, are there any resources …

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## [Finding a midpoint between a line](https://discourse.slicer.org/t/finding-a-midpoint-between-a-line/32678)

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**Author:** [@SlicerNewUser](https://discourse.slicer.org/u/SlicerNewUser)\
**Replies:** 2\
**Last updated:** [July 8, 2024, 11:39am UTC](https://discourse.slicer.org/t/finding-a-midpoint-between-a-line/32678 "2024-07-08T11:39:36Z")

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Hi there, If I make a Line in Markup (so there is 2 points). Is there anyway for the software to automatically mark another point that is the midpoint of that line? Thank you

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## [Liver tumor alignement](https://discourse.slicer.org/t/liver-tumor-alignement/37252)

<div class="topic-metadata">

**Author:** [@Noa](https://discourse.slicer.org/u/Noa)\
**Replies:** 0\
**Last updated:** [July 8, 2024, 8:43am UTC](https://discourse.slicer.org/t/liver-tumor-alignement/37252 "2024-07-08T08:43:08Z")

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Hello, I study liver tumors in different scan series and I am trying to compare their size, centroïds… Hence, I’m trying to do a segmentation on four volumes : CT scintigraphy and CT PET where I contour the liver sci…

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## [Error loading .mrml and associated .png files](https://discourse.slicer.org/t/error-loading-mrml-and-associated-png-files/37236)

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**Author:** [@pamelaeck](https://discourse.slicer.org/u/pamelaeck)\
**Replies:** 4\
**Last updated:** [July 7, 2024, 10:50pm UTC](https://discourse.slicer.org/t/error-loading-mrml-and-associated-png-files/37236 "2024-07-07T22:50:31Z")

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Slicer 5.6.2, MacBook Pro Ventura 13.6.7 I am newbie with using Slicer, hoping to run SlicerMorph for 3D morphometrics. I added some landmarks on a vertebra and saved. But when I try to open the .mrml and .png files I …

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## [Multiple Slicer instances in Windows 11 App list](https://discourse.slicer.org/t/multiple-slicer-instances-in-windows-11-app-list/37228)

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**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 1\
**Last updated:** [July 6, 2024, 3:00pm UTC](https://discourse.slicer.org/t/multiple-slicer-instances-in-windows-11-app-list/37228 "2024-07-06T15:00:00Z")

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How should I handle those ? Uninstall?

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## [Non Orthogonal reslice](https://discourse.slicer.org/t/non-orthogonal-reslice/37213)

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**Author:** [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)\
**Replies:** 2\
**Last updated:** [July 6, 2024, 7:02am UTC](https://discourse.slicer.org/t/non-orthogonal-reslice/37213 "2024-07-06T07:02:55Z")

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Hi, I never found a way to perform a non orthogonal reslice easily. I found that other people face the same problem, for instance : 1000\_tiny\_slices \[3d\](https://discourse.slicer.org/t/resample-image-volume-along-user-…

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## [Cloud instance ALPACA not working](https://discourse.slicer.org/t/cloud-instance-alpaca-not-working/37225)

<div class="topic-metadata">

**Author:** [@megvdb](https://discourse.slicer.org/u/megvdb)\
**Replies:** 1\
**Last updated:** [July 6, 2024, 2:38am UTC](https://discourse.slicer.org/t/cloud-instance-alpaca-not-working/37225 "2024-07-06T02:38:45Z")

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Hi! I have ply’s of 20 different scales in slicer and I am trying to use ALPACA to transfer the LM’s from one model to the rest but it wont run on the cloud. I am getting no error it just crashes. It works on my computer…

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## [Problem with segment editor paint](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109)

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**Author:** [@Ash\_Alarfaj](https://discourse.slicer.org/u/Ash_Alarfaj)\
**Replies:** 16\
**Last updated:** [July 5, 2024, 5:02pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109 "2024-07-05T17:02:43Z")

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Operating system:Windows Slicer version:4.9 Expected behavior: apply paint Actual behavior: doesn’t work! Hi could please help me, I start segmentation by applying the threshold, then correct it by paint and eras, b…

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