# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=45

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

**Page:** 46

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## [Adding a missing landmark to a mrk.json file ](https://discourse.slicer.org/t/adding-a-missing-landmark-to-a-mrk-json-file/42400)

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**Author:** [@grega](https://discourse.slicer.org/u/grega)\
**Replies:** 1\
**Last updated:** [April 3, 2025, 4:15am UTC](https://discourse.slicer.org/t/adding-a-missing-landmark-to-a-mrk-json-file/42400 "2025-04-03T04:15:46Z")

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I have a point on a bone that i’m landmarking that isn’t present on all the samples in my data set. To be able to run GPA+PCA analysis I need to have a consistent number of points for each sample, so is there a way I can…

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## [Slicer doesn't open after installing SlicerWMA extension](https://discourse.slicer.org/t/slicer-doesnt-open-after-installing-slicerwma-extension/42356)

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**Author:** [@Dmytro\_Shyshlov](https://discourse.slicer.org/u/Dmytro_Shyshlov)\
**Replies:** 5\
**Last updated:** [April 3, 2025, 12:44am UTC](https://discourse.slicer.org/t/slicer-doesnt-open-after-installing-slicerwma-extension/42356 "2025-04-03T00:44:42Z")

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Hello! I’m trying to run Slicer 5.8.1 on CentOS 7.9 server with 3 extensions: SlicerDMRI, SlicerWMA, UKFTractography. Everything works fine with DMRI and UKFT, but every time I try to install SlicerWMA the program doesn…

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## [Creating a boundary box after rotating/translating a volume](https://discourse.slicer.org/t/creating-a-boundary-box-after-rotating-translating-a-volume/42343)

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**Author:** [@coco](https://discourse.slicer.org/u/coco)\
**Replies:** 4\
**Last updated:** [April 2, 2025, 9:30am UTC](https://discourse.slicer.org/t/creating-a-boundary-box-after-rotating-translating-a-volume/42343 "2025-04-02T09:30:12Z")

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Dear all, I’m having some issues creating a bounding box arround my segment after registering a volume and segments. As you can see on the picture, the calculated bounding box “sticks” to the original volume geometry b…

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## [Sequence Browsing: Loss of Spatial Movement After Saving in Slicer](https://discourse.slicer.org/t/sequence-browsing-loss-of-spatial-movement-after-saving-in-slicer/42369)

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**Author:** [@rcpr](https://discourse.slicer.org/u/rcpr)\
**Replies:** 2\
**Last updated:** [April 1, 2025, 5:19pm UTC](https://discourse.slicer.org/t/sequence-browsing-loss-of-spatial-movement-after-saving-in-slicer/42369 "2025-04-01T17:19:03Z")

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Hi everyone! First of all, I’d like to thank you for your availability! I’m using fCal to receive ultrasound images from a frame grabber while simultaneously acquiring spatial information from the sensor attached to th…

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## [TotalSegmentator + "returned non-zero exit status 1."](https://discourse.slicer.org/t/totalsegmentator-returned-non-zero-exit-status-1/42395)

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**Author:** [@Camille\_Guillerminet](https://discourse.slicer.org/u/Camille_Guillerminet)\
**Replies:** 1\
**Last updated:** [April 1, 2025, 2:00pm UTC](https://discourse.slicer.org/t/totalsegmentator-returned-non-zero-exit-status-1/42395 "2025-04-01T14:00:48Z")

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Operating system: Windows 10 Slicer version:5.6.2 + CPU Dear support, I tried to run totalsegmentator but it failed after a while with the “returned non-zero exit status 1”. Could you help me to understand what is th…

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## [How to obtain the same SlicerElastix registration result outside 3DSlicer?](https://discourse.slicer.org/t/how-to-obtain-the-same-slicerelastix-registration-result-outside-3dslicer/42396)

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**Author:** [@lmariani](https://discourse.slicer.org/u/lmariani)\
**Replies:** 0\
**Last updated:** [April 1, 2025, 1:22pm UTC](https://discourse.slicer.org/t/how-to-obtain-the-same-slicerelastix-registration-result-outside-3dslicer/42396 "2025-04-01T13:22:54Z")

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OS: Windows 11 Slicer version: 5.9.0 When I perform a transformation using SlicerElastix I get a different result than the one I get using other Elastix libraries external to 3D Slicer. I tried to load the same paramet…

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## [TotalSegmentator + Slicer 5.8.1 - "ModuleNotFoundError: No module named 'pydicom.pixels'"](https://discourse.slicer.org/t/totalsegmentator-slicer-5-8-1-modulenotfounderror-no-module-named-pydicom-pixels/42386)

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**Author:** [@jochoaTX](https://discourse.slicer.org/u/jochoaTX)\
**Replies:** 2\
**Last updated:** [April 1, 2025, 12:05am UTC](https://discourse.slicer.org/t/totalsegmentator-slicer-5-8-1-modulenotfounderror-no-module-named-pydicom-pixels/42386 "2025-04-01T00:05:06Z")

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Operating system: WinPro 11 Slicer version: 5.8.1 Expected behavior: TotalSegmentator to totally segment Actual behavior: Pukes I’ve declared defeat. Cannot solve this myself. It seems that TotalSegmentator may be lo…

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## [Making hollow object solid ](https://discourse.slicer.org/t/making-hollow-object-solid/42240)

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**Author:** [@Jrneal241](https://discourse.slicer.org/u/Jrneal241)\
**Replies:** 5\
**Last updated:** [March 31, 2025, 11:30pm UTC](https://discourse.slicer.org/t/making-hollow-object-solid/42240 "2025-03-31T23:30:44Z")

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Hi, I am trying to 3D print a gill raker using a Formlabs resin printer. The gill raker is covered with mineralized structures (denticles), but the middle is completely hollow (b/c connective tissue). Currently, I have t…

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## [SlicerMorph Mean geometry getting flipped when exporting](https://discourse.slicer.org/t/slicermorph-mean-geometry-getting-flipped-when-exporting/42376)

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**Author:** [@Windy](https://discourse.slicer.org/u/Windy)\
**Replies:** 4\
**Last updated:** [March 31, 2025, 9:31pm UTC](https://discourse.slicer.org/t/slicermorph-mean-geometry-getting-flipped-when-exporting/42376 "2025-03-31T21:31:45Z")

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Hi all, I am using SlicerMorph’s GPA to get a mean shape from multiple geometries coming from multiple biological samples. I have registered my sample volumes to be in the same direction and then marked landmarks on the…

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## [Changing image spacing of image segmentations](https://discourse.slicer.org/t/changing-image-spacing-of-image-segmentations/42385)

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**Author:** [@jps](https://discourse.slicer.org/u/jps)\
**Replies:** 2\
**Last updated:** [March 31, 2025, 8:15pm UTC](https://discourse.slicer.org/t/changing-image-spacing-of-image-segmentations/42385 "2025-03-31T20:15:34Z")

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Hello! I mistakenly began segmenting on volumes without specifying the correct image spacing. Currently they are set to 1 mm and I learned how to change them to 0.002 mm by editing the volume properties. How do I apply…

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## [Saving transformed volumes and segmentations](https://discourse.slicer.org/t/saving-transformed-volumes-and-segmentations/41343)

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**Author:** [@jps](https://discourse.slicer.org/u/jps)\
**Replies:** 4\
**Last updated:** [March 31, 2025, 5:47pm UTC](https://discourse.slicer.org/t/saving-transformed-volumes-and-segmentations/41343 "2025-03-31T17:47:06Z")

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Hello, I have a lot of micro-CT scans that were scanned in different orientations. To get them all in the same orientation for facilitating segmentation, I transform the volumes following this tutorial: https://www.youtu…

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## [MONAI AutoSeg3D for CBCT (CMF)](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175)

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**Author:** [@ssingh](https://discourse.slicer.org/u/ssingh)\
**Replies:** 10\
**Last updated:** [March 31, 2025, 7:34am UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175 "2025-03-31T07:34:04Z")

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I tried MONAI AutoSeg3D auto-segmentation on CMF scan (CBCT). I see that the segmentation results appear like as if it was done on a downsampled image. Please see the snapshot here: I have used Whole Body segmentat…

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## [How to use 3dslicer software to accurately convert STL format files into nii format files](https://discourse.slicer.org/t/how-to-use-3dslicer-software-to-accurately-convert-stl-format-files-into-nii-format-files/42372)

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**Author:** [@lirongyaoper](https://discourse.slicer.org/u/lirongyaoper)\
**Replies:** 1\
**Last updated:** [March 30, 2025, 5:44pm UTC](https://discourse.slicer.org/t/how-to-use-3dslicer-software-to-accurately-convert-stl-format-files-into-nii-format-files/42372 "2025-03-30T17:44:01Z")

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Dear teacher, hello, recently I am doing 3D reconstruction, and some STL files need to be converted into NII format files. I tried to convert them through 3Dslicer software, but the results were not satisfactory. I woul…

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## [Weird volume rendering color](https://discourse.slicer.org/t/weird-volume-rendering-color/42296)

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**Author:** [@Arber\_Demi](https://discourse.slicer.org/u/Arber_Demi)\
**Replies:** 10\
**Last updated:** [March 29, 2025, 5:15pm UTC](https://discourse.slicer.org/t/weird-volume-rendering-color/42296 "2025-03-29T17:15:03Z")

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Hello everyone, I’m working on creating some form of “heatmap” on an existing volume. At the moment, I create 3D gaussian kernels of some value range (that I can target easily with the scalar color mapping) at specific …

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## [Segmenting a part of the tissue (colon, pouch) with very similar intensity to nearby structures](https://discourse.slicer.org/t/segmenting-a-part-of-the-tissue-colon-pouch-with-very-similar-intensity-to-nearby-structures/42359)

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**Author:** [@drhuzaifa](https://discourse.slicer.org/u/drhuzaifa)\
**Replies:** 0\
**Last updated:** [March 29, 2025, 4:16am UTC](https://discourse.slicer.org/t/segmenting-a-part-of-the-tissue-colon-pouch-with-very-similar-intensity-to-nearby-structures/42359 "2025-03-29T04:16:04Z")

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I have CT scan of the abdomen, and am trying to segment a “part” of the colon (pouch) along with the staple line, and since the pouch signal intensity very resembles nearby tissue, and using threshold gives lot of noise,…

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## [export coordinates of segmented plane .txt](https://discourse.slicer.org/t/export-coordinates-of-segmented-plane-txt/42358)

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**Author:** [@Gabby](https://discourse.slicer.org/u/Gabby)\
**Replies:** 0\
**Last updated:** [March 29, 2025, 4:15am UTC](https://discourse.slicer.org/t/export-coordinates-of-segmented-plane-txt/42358 "2025-03-29T04:15:32Z")

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Hi, I am very new to 3D Slicer. Someone told me that 3D Slicer can export the coordinates of a segmented plane. Can you please tell me, step by step, how to do that? I want to save the coordinates in a .txt file. Pleas…

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## [Lights module in Sandbox and Shadows](https://discourse.slicer.org/t/lights-module-in-sandbox-and-shadows/42347)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [March 29, 2025, 2:49am UTC](https://discourse.slicer.org/t/lights-module-in-sandbox-and-shadows/42347 "2025-03-29T02:49:36Z")

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I am trying to update our short course notes for the new shadow functionality in the preview. But it is not clear to me whether this is a full replacement of the Lights module in Sandbox. I tried to use them together and…

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## [Any way to reduce image stacks size?](https://discourse.slicer.org/t/any-way-to-reduce-image-stacks-size/42348)

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**Author:** [@JaredAmudeo](https://discourse.slicer.org/u/JaredAmudeo)\
**Replies:** 6\
**Last updated:** [March 28, 2025, 10:38pm UTC](https://discourse.slicer.org/t/any-way-to-reduce-image-stacks-size/42348 "2025-03-28T22:38:21Z")

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Hello! Recently, our research team has gained access to a benchtop micro-CT scanner, but the resulting files are very large, averaging over 10 GB. The output files are stacks of PNG and TIFF images. I am aware of the Cr…

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## [Skull base landmarking accuracy ALPACA](https://discourse.slicer.org/t/skull-base-landmarking-accuracy-alpaca/42279)

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**Author:** [@ThomasVanParys](https://discourse.slicer.org/u/ThomasVanParys)\
**Replies:** 12\
**Last updated:** [March 28, 2025, 9:46pm UTC](https://discourse.slicer.org/t/skull-base-landmarking-accuracy-alpaca/42279 "2025-03-28T21:46:24Z")

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Hello, I have created ~100 3D surface models of male and female human skulls from the NMDID. I aim to quantify sexual dimorphism in size and shape: For size, I have calculated Endocranial Volume (ECV, cm3). For shape,…

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## [How can I get rid off a terminology i have previously imported](https://discourse.slicer.org/t/how-can-i-get-rid-off-a-terminology-i-have-previously-imported/42351)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [March 28, 2025, 9:16pm UTC](https://discourse.slicer.org/t/how-can-i-get-rid-off-a-terminology-i-have-previously-imported/42351 "2025-03-28T21:16:05Z")

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I have a couple different incomplete terminologies i have imported during some test that i would like to get rid off. I am not sure where these are saved, since some of these terminologies show in Slicer versions that I …

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## [Segmentation of Alveolar cleft](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 9\
**Last updated:** [March 28, 2025, 8:21pm UTC](https://discourse.slicer.org/t/segmentation-of-alveolar-cleft/15104 "2025-03-28T20:21:34Z")

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I am trying to find a predictable way to measure the volume of an alveolar bone cleft in cleft lip and palate children with CBCT. Several papers describe that they have done it but it is very vague. The main problem…

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## [Engraving with SegmentEditorExtraEffects](https://discourse.slicer.org/t/engraving-with-segmenteditorextraeffects/42338)

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**Author:** [@dsweldon](https://discourse.slicer.org/u/dsweldon)\
**Replies:** 1\
**Last updated:** [March 27, 2025, 10:29pm UTC](https://discourse.slicer.org/t/engraving-with-segmenteditorextraeffects/42338 "2025-03-27T22:29:25Z")

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Operating system: Windows 11 Slicer version: 5.6.2 I am having issues with the Engraving tool on the “SegmentEditorExtraEffects” extension. When I make the engraving or embossing, and then hit “apply” the engraving/emb…

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## [The exported label comes LAI while image is LAS](https://discourse.slicer.org/t/the-exported-label-comes-lai-while-image-is-las/42341)

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**Author:** [@Berk\_Gezgin](https://discourse.slicer.org/u/Berk_Gezgin)\
**Replies:** 0\
**Last updated:** [March 28, 2025, 7:24am UTC](https://discourse.slicer.org/t/the-exported-label-comes-lai-while-image-is-las/42341 "2025-03-28T07:24:10Z")

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I create a segmentation and then do a labeling on an images (.nii.gz). When I export by clicking on export at the bottom of the image, the label comes in LAI format. However, my image is LAS and I want the label to come …

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## [Performing Centerline Extraction with One Point Per Slice Constraint](https://discourse.slicer.org/t/performing-centerline-extraction-with-one-point-per-slice-constraint/42337)

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**Author:** [@le0nzim](https://discourse.slicer.org/u/le0nzim)\
**Replies:** 0\
**Last updated:** [March 28, 2025, 12:22am UTC](https://discourse.slicer.org/t/performing-centerline-extraction-with-one-point-per-slice-constraint/42337 "2025-03-28T00:22:19Z")

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Hello! I would like to ask whether there is a way to constraint the centerline of a tubular shape to only be comprised by one point per slice. If not, is my only option extracting the full centerline and then resample i…

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## [Pip installed Python packaged works on PythonSlicer terminal but not on Slicer console](https://discourse.slicer.org/t/pip-installed-python-packaged-works-on-pythonslicer-terminal-but-not-on-slicer-console/41596)

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**Author:** [@modenaxe](https://discourse.slicer.org/u/modenaxe)\
**Replies:** 13\
**Last updated:** [March 27, 2025, 11:13pm UTC](https://discourse.slicer.org/t/pip-installed-python-packaged-works-on-pythonslicer-terminal-but-not-on-slicer-console/41596 "2025-03-27T23:13:12Z")

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Hello, I would like to install a python wheel not available form Pypi that was built for Python 3.9.10, which is the same version I see on the Slicer Python console. As suggested in various other posts, I am installing …

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## [Why can't my engrave function be apply?](https://discourse.slicer.org/t/why-cant-my-engrave-function-be-apply/23809)

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**Author:** [@sunwei921119](https://discourse.slicer.org/u/sunwei921119)\
**Replies:** 7\
**Last updated:** [June 12, 2022, 7:54am UTC](https://discourse.slicer.org/t/why-cant-my-engrave-function-be-apply/23809 "2022-06-12T07:54:31Z")

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Hello, why can’t my engrave function be apply? I tried several versions of it. Is there anything wrong?

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## [Linux preview build is failing](https://discourse.slicer.org/t/linux-preview-build-is-failing/42330)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [March 27, 2025, 10:20pm UTC](https://discourse.slicer.org/t/linux-preview-build-is-failing/42330 "2025-03-27T22:20:54Z")

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@lassoan @Sam\_Horvath

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## [Cannot import name 'TypeIs' from 'typing\_extensions'](https://discourse.slicer.org/t/cannot-import-name-typeis-from-typing-extensions/42336)

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**Author:** [@Arash1](https://discourse.slicer.org/u/Arash1)\
**Replies:** 0\
**Last updated:** [March 27, 2025, 8:32pm UTC](https://discourse.slicer.org/t/cannot-import-name-typeis-from-typing-extensions/42336 "2025-03-27T20:32:22Z")

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Hello everyone. I am facing a problem that just started today!! Majority of my Slicer is not working. I might be wrong but does this have anything with the Corporate certificates? On different versions of the software, …

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## [Warning information about “Gyroguide“](https://discourse.slicer.org/t/warning-information-about-gyroguide/42272)

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**Author:** [@doc-xie](https://discourse.slicer.org/u/doc-xie)\
**Replies:** 4\
**Last updated:** [March 27, 2025, 2:49am UTC](https://discourse.slicer.org/t/warning-information-about-gyroguide/42272 "2025-03-27T02:49:21Z")

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Hi everyone, In module “Gyroguide”, after the markers setting, click “calculate”, the warning information showed as below:Traceback (most recent call last): File “/Applications/Slicer.app/Contents/Extensions-32448/Gyro…

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## [Allow engraving text on curved surfaces in Segment Editor](https://discourse.slicer.org/t/allow-engraving-text-on-curved-surfaces-in-segment-editor/28935)

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**Author:** [@kopachini](https://discourse.slicer.org/u/kopachini)\
**Replies:** 3\
**Last updated:** [March 27, 2025, 1:52am UTC](https://discourse.slicer.org/t/allow-engraving-text-on-curved-surfaces-in-segment-editor/28935 "2025-03-27T01:52:58Z")

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It would be nice if the text could follow the contour of the curved models. And also, the engraved/embossed text does not fall under the whole model’s smoothing effect, yet should stay sharp. Otherwise great feature.

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