# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=155

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

**Page:** 156

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## [Failed to export file after total segmentation (fast, on CPU)](https://discourse.slicer.org/t/failed-to-export-file-after-total-segmentation-fast-on-cpu/29814)

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**Author:** [@simoneb](https://discourse.slicer.org/u/simoneb)\
**Replies:** 7\
**Last updated:** [June 27, 2023, 12:44pm UTC](https://discourse.slicer.org/t/failed-to-export-file-after-total-segmentation-fast-on-cpu/29814 "2023-06-27T12:44:09Z")

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Problem report for Slicer 5.2.2 win-amd64: Hello, I am new to 3D Slicer (version 5.2.2) I ran totalsegmentator (fast on CPU) and then tried to export file, but failed. Thanks for any help Logs\[DEBUG\]\[Qt\] 03.06.2023 17:4…

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## [How to set "Irregular volume geometry" threshold?](https://discourse.slicer.org/t/how-to-set-irregular-volume-geometry-threshold/30201)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 10\
**Last updated:** [June 27, 2023, 7:34am UTC](https://discourse.slicer.org/t/how-to-set-irregular-volume-geometry-threshold/30201 "2023-06-27T07:34:45Z")

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Hello, our clinical DICOM images very often seem to end up having “irregular volume geometry” detected just above the threshold of 0.001 mm. This is a typical message I got today: \[Python\] Irregular volume geometry det…

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## [Building the ijk to RAS transform from a nrrd file](https://discourse.slicer.org/t/building-the-ijk-to-ras-transform-from-a-nrrd-file/1513)

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**Author:** [@dcantor](https://discourse.slicer.org/u/dcantor)\
**Replies:** 5\
**Last updated:** [June 27, 2023, 7:17am UTC](https://discourse.slicer.org/t/building-the-ijk-to-ras-transform-from-a-nrrd-file/1513 "2023-06-27T07:17:46Z")

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Hi Slicers, I am working on a project with Slicer generated nrrd files and after looking at the nrrd header I notice there is no info about the ijk to RAS matrix yet when I load that nrrd file into Slicer I obtain the m…

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## [Airway Segmentation is working fine on sample CT but raises an error when running on my CT ](https://discourse.slicer.org/t/airway-segmentation-is-working-fine-on-sample-ct-but-raises-an-error-when-running-on-my-ct/30235)

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**Author:** [@Matteboo](https://discourse.slicer.org/u/Matteboo)\
**Replies:** 1\
**Last updated:** [June 26, 2023, 5:10pm UTC](https://discourse.slicer.org/t/airway-segmentation-is-working-fine-on-sample-ct-but-raises-an-error-when-running-on-my-ct/30235 "2023-06-26T17:10:27Z")

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Hello, As I say in the title I’m using a toolbox (airway segmentation). When I use it on a CT from “Sample Data” the toolbox runs fine and give the appropriate results. However, when I try to run it on my CTs I have an …

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## [ITK registration factory library cannot be found](https://discourse.slicer.org/t/itk-registration-factory-library-cannot-be-found/30227)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 2\
**Last updated:** [June 26, 2023, 1:52pm UTC](https://discourse.slicer.org/t/itk-registration-factory-library-cannot-be-found/30227 "2023-06-26T13:52:19Z")

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Hi, I am using 3D Slicer 5.2.2 r31382 / fb46bd1 on an Ubuntu 22.04 machine. I am trying to launch the DWIConvert process from the command line: $DWIConvert --conversionMode FSLToNrrd --outputVolume $DWI --fslNIFTIFile …

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## [Previously available extensions no longer available on 5.2.2](https://discourse.slicer.org/t/previously-available-extensions-no-longer-available-on-5-2-2/30226)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 2\
**Last updated:** [June 26, 2023, 1:47pm UTC](https://discourse.slicer.org/t/previously-available-extensions-no-longer-available-on-5-2-2/30226 "2023-06-26T13:47:47Z")

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Hi, I am using 3D Slicer 5.2.2 r31382 / fb46bd1, and when trying to install the following extensions it seems like the do not exist in the extension database (no match is shown), and thus cannot be installed: DTI-Reg D…

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## [Rotate and translate a node around a specified point](https://discourse.slicer.org/t/rotate-and-translate-a-node-around-a-specified-point/30232)

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**Author:** [@IsabelW96](https://discourse.slicer.org/u/IsabelW96)\
**Replies:** 0\
**Last updated:** [June 26, 2023, 9:01am UTC](https://discourse.slicer.org/t/rotate-and-translate-a-node-around-a-specified-point/30232 "2023-06-26T09:01:02Z")

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Hi everyone, I’ve tried to transform a node around a specified point script to work. The models are illustrated below. The red one is the reference model with the defined centroid (F-1). I followed the video as desc…

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## [How to script into code data loading, 3D model generation and screen capture tasks](https://discourse.slicer.org/t/how-to-script-into-code-data-loading-3d-model-generation-and-screen-capture-tasks/30228)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 0\
**Last updated:** [June 26, 2023, 2:16am UTC](https://discourse.slicer.org/t/how-to-script-into-code-data-loading-3d-model-generation-and-screen-capture-tasks/30228 "2023-06-26T02:16:22Z")

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Hi, I’d like to be able to automate some tasks in 3D Slicer by calling its Python API from the command line: Loading structural (e.g. an T1w MRI) and segmentation files for a given subject. Making the data displayed a…

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## [Generate a 3D model from CT scan of a population](https://discourse.slicer.org/t/generate-a-3d-model-from-ct-scan-of-a-population/30205)

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**Author:** [@zariliusra](https://discourse.slicer.org/u/zariliusra)\
**Replies:** 1\
**Last updated:** [June 25, 2023, 5:29pm UTC](https://discourse.slicer.org/t/generate-a-3d-model-from-ct-scan-of-a-population/30205 "2023-06-25T17:29:18Z")

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What is the best way to generate a 3D model of bone that represent various 3D model from CT scan of a population? Operating system: windows Slicer version:5.2.2 Expected behavior: Actual behavior:

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## [Does the slicer have a CBCT reconstruction module？](https://discourse.slicer.org/t/does-the-slicer-have-a-cbct-reconstruction-module/30218)

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**Author:** [@ma1282029525](https://discourse.slicer.org/u/ma1282029525)\
**Replies:** 2\
**Last updated:** [June 25, 2023, 5:27pm UTC](https://discourse.slicer.org/t/does-the-slicer-have-a-cbct-reconstruction-module/30218 "2023-06-25T17:27:24Z")

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Does the slicer have a CBCT reconstruction module？

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## [The colormap in "Volume Rendering" is wrong when using "fMRI" lookup table in "Volume"](https://discourse.slicer.org/t/the-colormap-in-volume-rendering-is-wrong-when-using-fmri-lookup-table-in-volume/30186)

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**Author:** [@ffr](https://discourse.slicer.org/u/ffr)\
**Replies:** 1\
**Last updated:** [June 24, 2023, 7:27pm UTC](https://discourse.slicer.org/t/the-colormap-in-volume-rendering-is-wrong-when-using-fmri-lookup-table-in-volume/30186 "2023-06-24T19:27:17Z")

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Operating system: Windows 11 Slicer version: 5.3.0 Expected behavior: fMRI colormap in “Volume Rendering” Actual behavior: Looks like it is using the “Warm2” colormap. Thank you very much.

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## [Help in setting up a script for CT image feature extraction with input as .npy files](https://discourse.slicer.org/t/help-in-setting-up-a-script-for-ct-image-feature-extraction-with-input-as-npy-files/30208)

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**Author:** [@Silke77](https://discourse.slicer.org/u/Silke77)\
**Replies:** 0\
**Last updated:** [June 24, 2023, 2:10pm UTC](https://discourse.slicer.org/t/help-in-setting-up-a-script-for-ct-image-feature-extraction-with-input-as-npy-files/30208 "2023-06-24T14:10:35Z")

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Dear all, is here someone i can talk to, who can help me with the start of uploading my data (.npy) in pyradiomics and extract features? the data is pre segmented CT images, which need to be loaded in python and i want …

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## [Any way to edit before converting to segmentation node?](https://discourse.slicer.org/t/any-way-to-edit-before-converting-to-segmentation-node/30196)

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**Author:** [@telomere](https://discourse.slicer.org/u/telomere)\
**Replies:** 2\
**Last updated:** [June 24, 2023, 2:27pm UTC](https://discourse.slicer.org/t/any-way-to-edit-before-converting-to-segmentation-node/30196 "2023-06-24T14:27:34Z")

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I loaded my STL file as model and I tried to convert it to segmentation nodes in a data module but slicer got freezed because the my STL file is too heavy. So I want to cut unneccessary part away before converting it to…

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## [Segmentation and feature extraction of brain tumors](https://discourse.slicer.org/t/segmentation-and-feature-extraction-of-brain-tumors/30209)

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**Author:** [@D-analyst\_Data\_Hub](https://discourse.slicer.org/u/D-analyst_Data_Hub)\
**Replies:** 0\
**Last updated:** [June 24, 2023, 10:58am UTC](https://discourse.slicer.org/t/segmentation-and-feature-extraction-of-brain-tumors/30209 "2023-06-24T10:58:57Z")

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Hello, I am also working on segmentation and feature extraction of MRI scans for brain tumors and need to decide on the best algorithms to use. I would appreciate if you could share your paper with me too. Thanks.

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## [Segmentation algorithm used in 3D Slicer](https://discourse.slicer.org/t/segmentation-algorithm-used-in-3d-slicer/7420)

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**Author:** [@sara04](https://discourse.slicer.org/u/sara04)\
**Replies:** 13\
**Last updated:** [September 1, 2019, 2:08pm UTC](https://discourse.slicer.org/t/segmentation-algorithm-used-in-3d-slicer/7420 "2019-09-01T14:08:02Z")

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Hi, I’m using 3D Slicer for tooth segmentation and I’ve created an stl model from ct scan (DICOM). I’ve done that using Segment editor module. Can someone tell me which segmentation algorithm is used in slicer to cre…

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## [TotalSegmentator setup](https://discourse.slicer.org/t/totalsegmentator-setup/26683)

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**Author:** [@Chuns\_SS](https://discourse.slicer.org/u/Chuns_SS)\
**Replies:** 27\
**Last updated:** [June 23, 2023, 12:14pm UTC](https://discourse.slicer.org/t/totalsegmentator-setup/26683 "2023-06-23T12:14:16Z")

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I keep getting errors trying to run totalsegmenter. I suspect it has to do with pyTorch not being installed properly on my system. Linux Ubuntu 22.04. To install pyTorch seems a bit tricky and most sites recommend using …

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## [Segment Comparison Tables: more than one comparison in a single table](https://discourse.slicer.org/t/segment-comparison-tables-more-than-one-comparison-in-a-single-table/18726)

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**Author:** [@liam-stubbington](https://discourse.slicer.org/u/liam-stubbington)\
**Replies:** 7\
**Last updated:** [June 23, 2023, 4:25am UTC](https://discourse.slicer.org/t/segment-comparison-tables-more-than-one-comparison-in-a-single-table/18726 "2023-06-23T04:25:48Z")

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Hi, I’m hugely impressed with SlicerRT’s segment comparison module. We are fortunate enough to have two independent clinical automatic segmentation algorithms - i’d like to use SlicerRT to compare the homologous struct…

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## [Assign a specific volume into slice](https://discourse.slicer.org/t/assign-a-specific-volume-into-slice/26848)

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**Author:** [@Jinhee\_Jang](https://discourse.slicer.org/u/Jinhee_Jang)\
**Replies:** 6\
**Last updated:** [June 23, 2023, 1:05am UTC](https://discourse.slicer.org/t/assign-a-specific-volume-into-slice/26848 "2023-06-23T01:05:04Z")

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Hi, I have a short question. I am browsing multiple MR images at the same time. After loading multiple images (usually done by drag and drop), I want to assign a specific volume using its IDs (such as ‘vtkMRMLScalarVol…

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## [Slicer to Matlab IGTLink Connection](https://discourse.slicer.org/t/slicer-to-matlab-igtlink-connection/30189)

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**Author:** [@LauraConnolly1](https://discourse.slicer.org/u/LauraConnolly1)\
**Replies:** 1\
**Last updated:** [June 23, 2023, 12:38am UTC](https://discourse.slicer.org/t/slicer-to-matlab-igtlink-connection/30189 "2023-06-23T00:38:05Z")

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Hi there! We’re trying to connect 3D Slicer to Matlab using a controller code written in 2018. I’m a bit confused about how to set up the server connection from 3D Slicer to Matlab in the Matlab Commander module. We cha…

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## [Export Markup sequence](https://discourse.slicer.org/t/export-markup-sequence/30184)

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**Author:** [@cams2b](https://discourse.slicer.org/u/cams2b)\
**Replies:** 0\
**Last updated:** [June 22, 2023, 5:53pm UTC](https://discourse.slicer.org/t/export-markup-sequence/30184 "2023-06-22T17:53:23Z")

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Hello everyone, I am trying to export a sequence of markup points. Currently when I try to right click on the sequence it only exports the markup for the current scene. I believe that my solution will require me to use …

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## [Cardiac Electrophysiology module not shown](https://discourse.slicer.org/t/cardiac-electrophysiology-module-not-shown/29811)

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**Author:** [@Julien\_D](https://discourse.slicer.org/u/Julien_D)\
**Replies:** 2\
**Last updated:** [June 22, 2023, 4:24pm UTC](https://discourse.slicer.org/t/cardiac-electrophysiology-module-not-shown/29811 "2023-06-22T16:24:25Z")

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Hi, I just installed EAMap Reader but the Electrophysiology Module doesn’t show in my list even after restart. It’s not in the settings list either (I’ve checked the Show hidden module just in case). Also, the module’s …

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## [3D model creation through multiple image slices](https://discourse.slicer.org/t/3d-model-creation-through-multiple-image-slices/30175)

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**Author:** [@LavaBunny](https://discourse.slicer.org/u/LavaBunny)\
**Replies:** 2\
**Last updated:** [June 22, 2023, 3:45pm UTC](https://discourse.slicer.org/t/3d-model-creation-through-multiple-image-slices/30175 "2023-06-22T15:45:04Z")

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After trying multiple tools, I think this tool may work for my project. Is this software able to take a set of 2D images and create a 3D model by stacking the 2D images one on top of another? Sorry if this question is s…

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## [Why sagittal yellow bar direction is "L"?](https://discourse.slicer.org/t/why-sagittal-yellow-bar-direction-is-l/30166)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 5\
**Last updated:** [June 21, 2023, 7:14pm UTC](https://discourse.slicer.org/t/why-sagittal-yellow-bar-direction-is-l/30166 "2023-06-21T19:14:15Z")

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Since Slicer uses RAS coordinate system I wonder why “L” letter is used on the yellow 2D slice view bar? Shouldn’t it be “R” (and also multiply the number by -1)? I was very confused by this while analyzing some image …

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## [3 leaked semaphore objects to clean up at shutdown\_MONAILabel](https://discourse.slicer.org/t/3-leaked-semaphore-objects-to-clean-up-at-shutdown-monailabel/29069)

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**Author:** [@Spiros\_Karkavitsas](https://discourse.slicer.org/u/Spiros_Karkavitsas)\
**Replies:** 1\
**Last updated:** [June 21, 2023, 7:04pm UTC](https://discourse.slicer.org/t/3-leaked-semaphore-objects-to-clean-up-at-shutdown-monailabel/29069 "2023-06-21T19:04:38Z")

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Operating system:Windows 10 Pro Slicer version: 5.12 Hello everyone, I am using MONAI to train an algorithm. However, as I submit the labels and press the train button this message appeared today a couple of times on …

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## [Bone thickness mapping module was not working. what's the wrong?](https://discourse.slicer.org/t/bone-thickness-mapping-module-was-not-working-whats-the-wrong/29567)

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**Author:** [@jhchoi](https://discourse.slicer.org/u/jhchoi)\
**Replies:** 1\
**Last updated:** [June 21, 2023, 11:27am UTC](https://discourse.slicer.org/t/bone-thickness-mapping-module-was-not-working-whats-the-wrong/29567 "2023-06-21T11:27:13Z")

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Python 3.9.10 (main, Feb 22 2023, 01:07:37) \[MSC v.1930 64 bit (AMD64)\] on win32 TODO: implement cloud fingerprint store \[Qt\] libpng warning: iCCP: profile ‘ICC Profile’: ‘CMYK’: invalid ICC profile color space \[…

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## [Mirror copy of a segmentation](https://discourse.slicer.org/t/mirror-copy-of-a-segmentation/6143)

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**Author:** [@Lucas\_Formighieri](https://discourse.slicer.org/u/Lucas_Formighieri)\
**Replies:** 7\
**Last updated:** [June 21, 2023, 3:54am UTC](https://discourse.slicer.org/t/mirror-copy-of-a-segmentation/6143 "2023-06-21T03:54:12Z")

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Hello, I would like to know if it is possible to make a mirror copy of a segmentation. For example, I have the segmentation of the left side of a face and I want to make a “right” side of the same face. Thanks, Lucas

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## [Cannot open files or folders from within Slicer on Linux](https://discourse.slicer.org/t/cannot-open-files-or-folders-from-within-slicer-on-linux/30134)

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**Author:** [@benzwick](https://discourse.slicer.org/u/benzwick)\
**Replies:** 3\
**Last updated:** [June 20, 2023, 8:51pm UTC](https://discourse.slicer.org/t/cannot-open-files-or-folders-from-within-slicer-on-linux/30134 "2023-06-20T20:51:53Z")

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I’m using Slicer (stable 5.2.2 and preview 5.3.0-2023-06-17) on Debian 12 (bookworm) Linux with KDE. When I try to open a file using the “Edit” button in a ScriptedLoadableModule or a directory in e.g. the SlicerElastix …

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## [3D Visualization Method in Slicer](https://discourse.slicer.org/t/3d-visualization-method-in-slicer/30110)

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**Author:** [@DzungDinh](https://discourse.slicer.org/u/DzungDinh)\
**Replies:** 5\
**Last updated:** [June 20, 2023, 6:58pm UTC](https://discourse.slicer.org/t/3d-visualization-method-in-slicer/30110 "2023-06-20T18:58:22Z")

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Hello, I wonder what 3d visualization method using for reconstructing 3D segmentation in Slicer? (e.g., interpolation, …). Moreover, is there any way I can view the current method? FYI, I have the segmentation in 2D, a…

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## [Markups module lagging when placing anatomical landmarks](https://discourse.slicer.org/t/markups-module-lagging-when-placing-anatomical-landmarks/27529)

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**Author:** [@meganfveltri](https://discourse.slicer.org/u/meganfveltri)\
**Replies:** 17\
**Last updated:** [June 20, 2023, 6:48pm UTC](https://discourse.slicer.org/t/markups-module-lagging-when-placing-anatomical-landmarks/27529 "2023-06-20T18:48:02Z")

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Hello! I’m hoping to get some clarification on some issues I’ve been having with markups in Slicer. I am very new to using the program so any help is appreciated. I have two ages of mouse skulls (E17.5 and P28) for whic…

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## [Exporting sequence annotation (2d + time)](https://discourse.slicer.org/t/exporting-sequence-annotation-2d-time/30163)

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**Author:** [@cams2b](https://discourse.slicer.org/u/cams2b)\
**Replies:** 0\
**Last updated:** [June 20, 2023, 6:26pm UTC](https://discourse.slicer.org/t/exporting-sequence-annotation-2d-time/30163 "2023-06-20T18:26:58Z")

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I am a new user of 3d slicer and I am working on segmenting 2d + time sequences. I have successfully annotated the sequences and I have saved the annotations as sequence files. I am now trying to export the annotations t…

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