# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=70

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

**Page:** 71

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## [Issue with Saving Files](https://discourse.slicer.org/t/issue-with-saving-files/39722)

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**Author:** [@Marta\_Fernandez](https://discourse.slicer.org/u/Marta_Fernandez)\
**Replies:** 5\
**Last updated:** [October 17, 2024, 3:15am UTC](https://discourse.slicer.org/t/issue-with-saving-files/39722 "2024-10-17T03:15:09Z")

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I’m experiencing a strange issue with 3D Slicer 5.7 version. When I save a file in the program’s format to continue working later, the following happens: If I save the file on the desktop, it reopens exactly as I left it…

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## [Lung tumor segmentation and feature extraction using pyradiomics and python](https://discourse.slicer.org/t/lung-tumor-segmentation-and-feature-extraction-using-pyradiomics-and-python/29963)

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**Author:** [@Ridwanur\_Rahman](https://discourse.slicer.org/u/Ridwanur_Rahman)\
**Replies:** 2\
**Last updated:** [October 16, 2024, 7:16pm UTC](https://discourse.slicer.org/t/lung-tumor-segmentation-and-feature-extraction-using-pyradiomics-and-python/29963 "2024-10-16T19:16:46Z")

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Hello Altruists, I’m doing a project on tumor segmentation of the lung. I’ve got only the Dicom images. My job is the find the ROI to segment only the tumor part and extract features using pyradiomics, later run ML mode…

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## ["tuple index out of range" and "could not convert string to float" - Musculoskeletal Analysis](https://discourse.slicer.org/t/tuple-index-out-of-range-and-could-not-convert-string-to-float-musculoskeletal-analysis/39728)

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**Author:** [@sp01](https://discourse.slicer.org/u/sp01)\
**Replies:** 0\
**Last updated:** [October 16, 2024, 6:20pm UTC](https://discourse.slicer.org/t/tuple-index-out-of-range-and-could-not-convert-string-to-float-musculoskeletal-analysis/39728 "2024-10-16T18:20:08Z")

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I was hoping to use the Musculoskeletal Analysis Extension, specifically the Density Analysis function, for a project, but I’m having trouble getting it to run in practice tests. When I run the Density Analysis on the e…

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## [MonaiLabel server](https://discourse.slicer.org/t/monailabel-server/39726)

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**Author:** [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)\
**Replies:** 0\
**Last updated:** [October 16, 2024, 3:45pm UTC](https://discourse.slicer.org/t/monailabel-server/39726 "2024-10-16T15:45:08Z")

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I don’t know how to create a MONAI Label server on my Mac. My purpose is to train a model on a set of CT scans I have in .nrrd files. Thanks for any help, best.

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## [Temporal calibration in 3D slicer](https://discourse.slicer.org/t/temporal-calibration-in-3d-slicer/33876)

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**Author:** [@MReza](https://discourse.slicer.org/u/MReza)\
**Replies:** 7\
**Last updated:** [October 16, 2024, 9:13am UTC](https://discourse.slicer.org/t/temporal-calibration-in-3d-slicer/33876 "2024-10-16T09:13:17Z")

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Hello, I’m wondering if it’s possible to perform temporal calibration in 3D Slicer as well. According to the Slicer IGT tutorial, temporal calibration seems to require the use of fCal. However, using fCal for temporal c…

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## [Creating non-manifold assembly and projecting mesh](https://discourse.slicer.org/t/creating-non-manifold-assembly-and-projecting-mesh/39701)

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**Author:** [@farhanm](https://discourse.slicer.org/u/farhanm)\
**Replies:** 1\
**Last updated:** [October 15, 2024, 12:45am UTC](https://discourse.slicer.org/t/creating-non-manifold-assembly-and-projecting-mesh/39701 "2024-10-15T00:45:55Z")

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Hi everyone, I am a PhD student at the Weiss Biomechanics Lab, University of Utah. I am working on creating volumetric meshes from microCT scan images. Currently, I use MIMICS (v 24.0) for segmentation and 3-Matic (v 16…

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## [Segmentation of Eustechian tube from CT](https://discourse.slicer.org/t/segmentation-of-eustechian-tube-from-ct/39697)

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**Author:** [@vshe](https://discourse.slicer.org/u/vshe)\
**Replies:** 0\
**Last updated:** [October 14, 2024, 5:13pm UTC](https://discourse.slicer.org/t/segmentation-of-eustechian-tube-from-ct/39697 "2024-10-14T17:13:19Z")

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Hi All, I am currently working on a project to segment the eustachian tube from CT data. I am attempting to manually label the eustachian tube, but it has been quite challenging to accurately locate and label it. Does …

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## [Configure ROI to match volume through code](https://discourse.slicer.org/t/configure-roi-to-match-volume-through-code/39695)

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**Author:** [@shai-ikko](https://discourse.slicer.org/u/shai-ikko)\
**Replies:** 0\
**Last updated:** [October 14, 2024, 3:20pm UTC](https://discourse.slicer.org/t/configure-roi-to-match-volume-through-code/39695 "2024-10-14T15:20:40Z")

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Hi, I’m trying to use a ROI markup to designate a rotation transform (I don’t want an actual transform because reasons). I initially configure the ROI as recommended in the script repository. The problem is that this se…

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## [DentalSegmentator fails with "RuntimeError: Invalid nnUNet configuration. Model folder is missing the following folds"](https://discourse.slicer.org/t/dentalsegmentator-fails-with-runtimeerror-invalid-nnunet-configuration-model-folder-is-missing-the-following-folds/35697)

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**Author:** [@ARtur\_Zhumabekov](https://discourse.slicer.org/u/ARtur_Zhumabekov)\
**Replies:** 17\
**Last updated:** [October 14, 2024, 11:40am UTC](https://discourse.slicer.org/t/dentalsegmentator-fails-with-runtimeerror-invalid-nnunet-configuration-model-folder-is-missing-the-following-folds/35697 "2024-10-14T11:40:44Z")

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Hello I get this error Failed to load the segmentation. Check the inference folder content C:\\Users\\artur\\AppData\\Local\\Temp\\Slicer-vFmJLy\\output How i can fix it?

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## [How are dicom views flipped and rotated into the format used in 3d slicer?](https://discourse.slicer.org/t/how-are-dicom-views-flipped-and-rotated-into-the-format-used-in-3d-slicer/39676)

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**Author:** [@dj\_96](https://discourse.slicer.org/u/dj_96)\
**Replies:** 3\
**Last updated:** [October 13, 2024, 6:47pm UTC](https://discourse.slicer.org/t/how-are-dicom-views-flipped-and-rotated-into-the-format-used-in-3d-slicer/39676 "2024-10-13T18:47:13Z")

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In my own code when I load a dicom series with pydicom the slices are not necessarily in correct order and the 3 views are often flipped or rotated in a strange way. 3d Slicer seems to always correct it to a standard for…

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## [Need help with downloading weights for dental segmentator](https://discourse.slicer.org/t/need-help-with-downloading-weights-for-dental-segmentator/39670)

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**Author:** [@Yamansul](https://discourse.slicer.org/u/Yamansul)\
**Replies:** 1\
**Last updated:** [October 12, 2024, 4:11pm UTC](https://discourse.slicer.org/t/need-help-with-downloading-weights-for-dental-segmentator/39670 "2024-10-12T16:11:59Z")

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having a problem while download weights in dental segmentator and couldnt know how to download it manually, any one who can assist me please

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## [Automatic knee segmentation in MRI](https://discourse.slicer.org/t/automatic-knee-segmentation-in-mri/39668)

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**Author:** [@JulianZulu](https://discourse.slicer.org/u/JulianZulu)\
**Replies:** 1\
**Last updated:** [October 12, 2024, 3:52pm UTC](https://discourse.slicer.org/t/automatic-knee-segmentation-in-mri/39668 "2024-10-12T15:52:01Z")

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Hello, I have a 3DMRI dataset of the same knee with the following scan types with acquisition matrix 0\\512\\350\\0 and slice thickness of 0.74mm. PD (TE: 35, TR:1100) PD FS (TE: 35, TR:1100) DESS (TE: 5.3, TR: 14.8) Do…

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## [How can jupyter control all the slicer](https://discourse.slicer.org/t/how-can-jupyter-control-all-the-slicer/39592)

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**Author:** [@VirOrange](https://discourse.slicer.org/u/VirOrange)\
**Replies:** 2\
**Last updated:** [October 12, 2024, 1:34pm UTC](https://discourse.slicer.org/t/how-can-jupyter-control-all-the-slicer/39592 "2024-10-12T13:34:42Z")

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Hi everyone, I am new to Slicer and would like to understand how Jupyter can be used to control Slicer. Specifically: Does using Jupyter mean that I can debug and trace the execution of different modules within Slicer…

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## [Creating a 3D Slicer extension with minimal programming skills](https://discourse.slicer.org/t/creating-a-3d-slicer-extension-with-minimal-programming-skills/17208)

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**Author:** [@Vincebisca](https://discourse.slicer.org/u/Vincebisca)\
**Replies:** 48\
**Last updated:** [October 12, 2024, 1:27am UTC](https://discourse.slicer.org/t/creating-a-3d-slicer-extension-with-minimal-programming-skills/17208 "2024-10-12T01:27:16Z")

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Operating system: Win64 Slicer version: 4.11 Hello, I am an Engineering Student, with a background in CAD Softwares and Product Design. Recently, for an internship project, I started to use 3D Slicer to perform segmen…

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## [How to start to edit a markups control point position interactively with code](https://discourse.slicer.org/t/how-to-start-to-edit-a-markups-control-point-position-interactively-with-code/39661)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 2\
**Last updated:** [October 11, 2024, 9:52pm UTC](https://discourse.slicer.org/t/how-to-start-to-edit-a-markups-control-point-position-interactively-with-code/39661 "2024-10-11T21:52:41Z")

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Hi My requirement is to have 3 points with labels “A”, “B” and “C”; and have a GUI with 3 checkable buttons with texts “A”, “B” and “C”. When a button is checked then interactive mode should allow to edit point position…

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## [TotalSegmentator install fails at nnunetv2 installation](https://discourse.slicer.org/t/totalsegmentator-install-fails-at-nnunetv2-installation/39663)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 8\
**Last updated:** [October 11, 2024, 9:39pm UTC](https://discourse.slicer.org/t/totalsegmentator-install-fails-at-nnunetv2-installation/39663 "2024-10-11T21:39:53Z")

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I want to try out the TotalSegmentator extension, however I can’t get it to run. From a clean install of the most recent Slicer preview on Windows (5.7.0-2024-10-08), I installed TotalSegmentator extension plus other bo…

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## [Combining .fcsv Files](https://discourse.slicer.org/t/combining-fcsv-files/39662)

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**Author:** [@EBaxter](https://discourse.slicer.org/u/EBaxter)\
**Replies:** 1\
**Last updated:** [October 11, 2024, 6:38pm UTC](https://discourse.slicer.org/t/combining-fcsv-files/39662 "2024-10-11T18:38:47Z")

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Hi, I have been assigning both fixed and semi landmarks to a skull, and I now saved these as a .fcsv file so that I can carry these forward for a GPA/PCA in SlicerMorph. Given that I have separate semilandmark curves o…

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## [CT vessel contouring](https://discourse.slicer.org/t/ct-vessel-contouring/39657)

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**Author:** [@LuKo](https://discourse.slicer.org/u/LuKo)\
**Replies:** 1\
**Last updated:** [October 11, 2024, 6:33pm UTC](https://discourse.slicer.org/t/ct-vessel-contouring/39657 "2024-10-11T18:33:39Z")

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Dear 3D slicer experts Dear All, I am looking for way to contour arteries on CT images, to mark the lumen and vessel. Any hints on how to do it, or what extension to use? Thank you!

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## [ALPACA "What is the Target landmark set used for?"](https://discourse.slicer.org/t/alpaca-what-is-the-target-landmark-set-used-for/39648)

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**Author:** [@Chuan](https://discourse.slicer.org/u/Chuan)\
**Replies:** 2\
**Last updated:** [October 11, 2024, 6:19pm UTC](https://discourse.slicer.org/t/alpaca-what-is-the-target-landmark-set-used-for/39648 "2024-10-11T18:19:54Z")

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Hi, I have a question regarding on the option of “Target landmark set (Optional)”, does anyone know what is this used for? Since ALPACA can generate new landmark on Target model, why there is this option that allowing…

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## [Save Scenes in the same file](https://discourse.slicer.org/t/save-scenes-in-the-same-file/39582)

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**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 3\
**Last updated:** [October 8, 2024, 2:05pm UTC](https://discourse.slicer.org/t/save-scenes-in-the-same-file/39582 "2024-10-08T14:05:20Z")

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Hi to everyone, me and my team are trying to save the scene in the same directory where we have saved the scene before. def saveScene(self): """ Saves the current MRML scene to the specified dir…

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## [Slicer 5.6.2 will flash back when it calculated Hausdorff metric and Dice metric in SegmentComparison module](https://discourse.slicer.org/t/slicer-5-6-2-will-flash-back-when-it-calculated-hausdorff-metric-and-dice-metric-in-segmentcomparison-module/39552)

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**Author:** [@Alice914](https://discourse.slicer.org/u/Alice914)\
**Replies:** 9\
**Last updated:** [October 11, 2024, 1:26pm UTC](https://discourse.slicer.org/t/slicer-5-6-2-will-flash-back-when-it-calculated-hausdorff-metric-and-dice-metric-in-segmentcomparison-module/39552 "2024-10-11T13:26:44Z")

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Slicer will flash back when calculating Hausdorff distance metrics and dice metrics for the same layer in two different images using slicer’s radiotherapy-segmentcomparison. I tried to reduce the size of the image and ru…

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## [Select complex area for segmentation](https://discourse.slicer.org/t/select-complex-area-for-segmentation/39640)

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**Author:** [@Thomas\_Bourdeau](https://discourse.slicer.org/u/Thomas_Bourdeau)\
**Replies:** 1\
**Last updated:** [October 11, 2024, 1:12pm UTC](https://discourse.slicer.org/t/select-complex-area-for-segmentation/39640 "2024-10-11T13:12:00Z")

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Hello Everyone, I hope this message will reach someone who can help me. I am doing micro CT for space material application. I am looking for a way to only process segmentation in a specific area. The objective is to me…

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## [3D Slicer can not open again](https://discourse.slicer.org/t/3d-slicer-can-not-open-again/39628)

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**Author:** [@doc-xie](https://discourse.slicer.org/u/doc-xie)\
**Replies:** 7\
**Last updated:** [October 11, 2024, 12:13pm UTC](https://discourse.slicer.org/t/3d-slicer-can-not-open-again/39628 "2024-10-11T12:13:14Z")

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After some modules installed, 3D Slicer can not open with the following information: ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: …

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## [Segmentation editor not working](https://discourse.slicer.org/t/segmentation-editor-not-working/39654)

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**Author:** [@Giovanni\_Nicoletto](https://discourse.slicer.org/u/Giovanni_Nicoletto)\
**Replies:** 1\
**Last updated:** [October 11, 2024, 12:09pm UTC](https://discourse.slicer.org/t/segmentation-editor-not-working/39654 "2024-10-11T12:09:19Z")

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Hi everyone, I was trying to create a segmentation of a face from a full head file. The problem Is that when I try to edit my new segmentation, threshold, scissor and all the other tools don’t affect the head. I think I…

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## [CRIPPLING LAG during segmentation on a strong computer](https://discourse.slicer.org/t/crippling-lag-during-segmentation-on-a-strong-computer/37218)

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**Author:** [@hari\_seldon](https://discourse.slicer.org/u/hari_seldon)\
**Replies:** 18\
**Last updated:** [July 9, 2024, 6:50pm UTC](https://discourse.slicer.org/t/crippling-lag-during-segmentation-on-a-strong-computer/37218 "2024-07-09T18:50:47Z")

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Hello, getting desperate here. I am in the Segment Editor removing voxels from 256x256x256 cubes in the 3D viewport. I engage the eraser tool and select “sphere brush” and “edit in 3D views”, and then when I go into the …

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## [Reading a micro-Ct scans based on attenuation coefficient and knowing the attenuation coeeficient](https://discourse.slicer.org/t/reading-a-micro-ct-scans-based-on-attenuation-coefficient-and-knowing-the-attenuation-coeeficient/39642)

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**Author:** [@sam5](https://discourse.slicer.org/u/sam5)\
**Replies:** 1\
**Last updated:** [October 10, 2024, 8:04pm UTC](https://discourse.slicer.org/t/reading-a-micro-ct-scans-based-on-attenuation-coefficient-and-knowing-the-attenuation-coeeficient/39642 "2024-10-10T20:04:33Z")

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I have a question, I have a series of micro CT scans, based on attenuation coefficient, and want to that and then transfer t to HU

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## [GPA module not executing ](https://discourse.slicer.org/t/gpa-module-not-executing/34583)

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**Author:** [@megvdb](https://discourse.slicer.org/u/megvdb)\
**Replies:** 10\
**Last updated:** [October 10, 2024, 7:07pm UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583 "2024-10-10T19:07:00Z")

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Operating system: Mac OS Slicer version: 5.6.0 Expected behavior: Trying to execute GPA+PCA Actual behavior: wont run! Hi! I have used ALPACA to get landmarks for 9 species and I selected these files in the GPA modul…

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## [Visualization of a vtk file](https://discourse.slicer.org/t/visualization-of-a-vtk-file/39629)

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**Author:** [@lolamartinalonso](https://discourse.slicer.org/u/lolamartinalonso)\
**Replies:** 1\
**Last updated:** [October 10, 2024, 1:49pm UTC](https://discourse.slicer.org/t/visualization-of-a-vtk-file/39629 "2024-10-10T13:49:33Z")

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Hi community, I am trying to open a vtk file in 3DSlicer. I open it as Model, and then in the Model module I try to visualize it but I can not see anything. In Paraview I have to visualize it as Point Gaussian. Can yo…

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## [Using Ge Vscan Extend](https://discourse.slicer.org/t/using-ge-vscan-extend/39469)

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**Author:** [@ruben99999](https://discourse.slicer.org/u/ruben99999)\
**Replies:** 1\
**Last updated:** [October 10, 2024, 12:45pm UTC](https://discourse.slicer.org/t/using-ge-vscan-extend/39469 "2024-10-10T12:45:24Z")

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Hello, I am a biomedical engineering graduate student, and for my master’s thesis project, I need to use the GE Vscan Extend ultrasound probe along with the NDI Aurora tracking system. What is required of me is to use th…

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## [Reload module error](https://discourse.slicer.org/t/reload-module-error/39581)

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**Author:** [@Shirly\_Someck](https://discourse.slicer.org/u/Shirly_Someck)\
**Replies:** 5\
**Last updated:** [October 10, 2024, 11:44am UTC](https://discourse.slicer.org/t/reload-module-error/39581 "2024-10-10T11:44:27Z")

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Hi, I’ve been using slicer a few months now, and recently trying to write an extension. Yesterday I moved some of my python files to a new path (since I had trouble importing them to my project), and since then I can’t…

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