# \#slicermorph

**URL:** https://discourse.slicer.org/tag/slicermorph/239.md

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

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## [Question on Segmentation and Smoothing a Gecko Skull](https://discourse.slicer.org/t/question-on-segmentation-and-smoothing-a-gecko-skull/47990)

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**Author:** [@GBurkin](https://discourse.slicer.org/u/GBurkin)\
**Replies:** 2\
**Last updated:** [August 26, 2026, 6:51pm UTC](https://discourse.slicer.org/t/question-on-segmentation-and-smoothing-a-gecko-skull/47990 "2026-08-26T18:51:15Z")

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Hello, I’m working with CT scans of small geckos, and I’m working on segmenting their skulls and full skeletons. I have mostly taught myself how to segment via YouTube and help pages, but most of these are focused on hu…

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## [Problem using MEMOS extension](https://discourse.slicer.org/t/problem-using-memos-extension/34456)

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**Author:** [@coco](https://discourse.slicer.org/u/coco)\
**Replies:** 25\
**Last updated:** [July 29, 2026, 5:00pm UTC](https://discourse.slicer.org/t/problem-using-memos-extension/34456 "2026-07-29T17:00:51Z")

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Dear Murat, very excited to use this tool for tests but I seem to be stuck. Most likely a problem with my environment but any suggestion or help appreciated. I installed a fresh version of slicer (5.6.1) on windows 11.…

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## [Smallest specimen possible to image with Slicer Photogrammetry?](https://discourse.slicer.org/t/smallest-specimen-possible-to-image-with-slicer-photogrammetry/47522)

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**Author:** [@imfeldts001](https://discourse.slicer.org/u/imfeldts001)\
**Replies:** 5\
**Last updated:** [July 10, 2026, 5:38pm UTC](https://discourse.slicer.org/t/smallest-specimen-possible-to-image-with-slicer-photogrammetry/47522 "2026-07-10T17:38:57Z")

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Greetings! My students and I have begun a project using Slicer Photogrammetry to create 3D models of songbird skulls from natural history collection in the area. The platform has worked well for us with the largest spec…

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## [Partial GPA idea for slicermorph](https://discourse.slicer.org/t/partial-gpa-idea-for-slicermorph/47387)

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**Author:** [@Stephan\_Collins](https://discourse.slicer.org/u/Stephan_Collins)\
**Replies:** 3\
**Last updated:** [June 19, 2026, 5:24pm UTC](https://discourse.slicer.org/t/partial-gpa-idea-for-slicermorph/47387 "2026-06-19T17:24:27Z")

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Dear all, Dear all, I am writing from a conference where I am learning a great deal about morphogeometry, which is quite far from my original background. One issue that has come up, and that I have also encountered wh…

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## [Animator module not exporting in any format](https://discourse.slicer.org/t/animator-module-not-exporting-in-any-format/47153)

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**Author:** [@Atticus](https://discourse.slicer.org/u/Atticus)\
**Replies:** 6\
**Last updated:** [May 28, 2026, 4:41pm UTC](https://discourse.slicer.org/t/animator-module-not-exporting-in-any-format/47153 "2026-05-28T16:41:54Z")

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I have used the Animator module in the past to produce short animations of volumes rotating, being cropped to ROIs or changing their colors. I have not been able to export animations today, in any format or resolution, …

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## [IDAVLM Converter Not Aligning Landmarks to Model](https://discourse.slicer.org/t/idavlm-converter-not-aligning-landmarks-to-model/46940)

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**Author:** [@ThomasVanParys](https://discourse.slicer.org/u/ThomasVanParys)\
**Replies:** 5\
**Last updated:** [May 7, 2026, 2:31pm UTC](https://discourse.slicer.org/t/idavlm-converter-not-aligning-landmarks-to-model/46940 "2026-05-07T14:31:45Z")

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Hello All, I have create a patch in Landmark IDAV, converting the .PTS in SlicerMorph IDAVLM converter. However, they do not align with the corresponding mesh used in Landmark as seen in the UI: I am clearly missing…

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## [Alpaca template selection K-means](https://discourse.slicer.org/t/alpaca-template-selection-k-means/45963)

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**Author:** [@Stephan\_Collins](https://discourse.slicer.org/u/Stephan_Collins)\
**Replies:** 1\
**Last updated:** [January 28, 2026, 3:52pm UTC](https://discourse.slicer.org/t/alpaca-template-selection-k-means/45963 "2026-01-28T15:52:21Z")

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Dear all, there’s something I did not understand in the ALPACA workflow. The plos one paper clearly explains the benefits of doing K means clustering and choosing templates that best match subgroups of data relative to …

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## [New arxiv paper about MorphoCloud](https://discourse.slicer.org/t/new-arxiv-paper-about-morphocloud/45628)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 9\
**Last updated:** [January 14, 2026, 5:47pm UTC](https://discourse.slicer.org/t/new-arxiv-paper-about-morphocloud/45628 "2026-01-14T17:47:47Z")

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@muratmaga and @jcfr have a new preprint out describing MorphoCloud :+1:

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## [Only points showing in Mean Shape Visualization - Slicermorph](https://discourse.slicer.org/t/only-points-showing-in-mean-shape-visualization-slicermorph/45121)

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**Author:** [@emmm\_m](https://discourse.slicer.org/u/emmm_m)\
**Replies:** 8\
**Last updated:** [November 21, 2025, 3:26am UTC](https://discourse.slicer.org/t/only-points-showing-in-mean-shape-visualization-slicermorph/45121 "2025-11-21T03:26:33Z")

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I’m new to slicer so I apologize if this is a question driven by my ineptness. I am working on generating GPA/PCA visualizations, however when I try to generate a Mean shape visualization for the proximal and distal end …

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## [Mirroring landmarks prior to GPA](https://discourse.slicer.org/t/mirroring-landmarks-prior-to-gpa/44457)

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**Author:** [@macorreia42](https://discourse.slicer.org/u/macorreia42)\
**Replies:** 2\
**Last updated:** [September 12, 2025, 2:57pm UTC](https://discourse.slicer.org/t/mirroring-landmarks-prior-to-gpa/44457 "2025-09-12T14:57:56Z")

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Dear Support, I have a number of incomplete mandibles on which I have placed landmarks prior to GM analyses. For each one, I only placed landmarks on the most complete side, so some .mrk.json have landmarks on a left ma…

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## [DeCAL: groupwise analysis](https://discourse.slicer.org/t/decal-groupwise-analysis/43742)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 14\
**Last updated:** [July 30, 2025, 3:48pm UTC](https://discourse.slicer.org/t/decal-groupwise-analysis/43742 "2025-07-30T15:48:45Z")

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Dear all, I would like to analyse two groups of skull-data, micro-CT data. The idea is to start with group1 run DeCAL with the data of group1, use the models and fixed LMs to generate an atlas and the alignedLMs (gro…

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## [Slicer crashing when trying to import image stacks using SlicerMorph](https://discourse.slicer.org/t/slicer-crashing-when-trying-to-import-image-stacks-using-slicermorph/43855)

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**Author:** [@Russell\_Engelman](https://discourse.slicer.org/u/Russell_Engelman)\
**Replies:** 11\
**Last updated:** [July 27, 2025, 6:39am UTC](https://discourse.slicer.org/t/slicer-crashing-when-trying-to-import-image-stacks-using-slicermorph/43855 "2025-07-27T06:39:24Z")

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Computer - Dell Precision 7710 Software OS - Windows 10 Pro Total RAM - 64 gB CPU - Intel(R) Xeon(R) CPU E3-1505M v5 @ 2.80 gHz GPU - NVIDIA Quadro M3000M Slicer Version - Slicer 5.8.1 My version of Slicer is crash…

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## [Variations in Volume: Segment Endocranium Utility in Slicermorph](https://discourse.slicer.org/t/variations-in-volume-segment-endocranium-utility-in-slicermorph/43747)

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**Author:** [@sck84](https://discourse.slicer.org/u/sck84)\
**Replies:** 1\
**Last updated:** [July 16, 2025, 8:23pm UTC](https://discourse.slicer.org/t/variations-in-volume-segment-endocranium-utility-in-slicermorph/43747 "2025-07-16T20:23:11Z")

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Hello, I am segmenting the endocranial cavity of mouse skulls using the Segment Endocranium utility in SlicerMorph. I noticed that there are pretty significant differences in the resulting segments when I run it a serie…

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## [Opening ALPACA for the first time and stuck on "Installing ALPACA Python Packages...."](https://discourse.slicer.org/t/opening-alpaca-for-the-first-time-and-stuck-on-installing-alpaca-python-packages/43415)

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**Author:** [@jsguerra](https://discourse.slicer.org/u/jsguerra)\
**Replies:** 3\
**Last updated:** [June 19, 2025, 4:37pm UTC](https://discourse.slicer.org/t/opening-alpaca-for-the-first-time-and-stuck-on-installing-alpaca-python-packages/43415 "2025-06-19T16:37:40Z")

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I recently upgraded my SSD and re-installed Slicermorph and the ALPACA extension. I went ahead and tried to open ALPACA for the first time since the new install and I seem to be stuck in the “Installing ALPACA Python Pac…

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## [Mirror landmarks and evaluate mandible asymmetry in DeCA](https://discourse.slicer.org/t/mirror-landmarks-and-evaluate-mandible-asymmetry-in-deca/43177)

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**Author:** [@yijie3091](https://discourse.slicer.org/u/yijie3091)\
**Replies:** 4\
**Last updated:** [June 10, 2025, 7:03am UTC](https://discourse.slicer.org/t/mirror-landmarks-and-evaluate-mandible-asymmetry-in-deca/43177 "2025-06-10T07:03:29Z")

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Dear professor，I have downloaded the DeCA and successfully used it to generate a mean mesh from mandible datasetes，but if I want to evaluate the mandible asymmetry across the midsaggital plane in the “Mirror Data” and “D…

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## [MorphoCloud Instance Issue](https://discourse.slicer.org/t/morphocloud-instance-issue/42645)

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**Author:** [@Ellie\_In](https://discourse.slicer.org/u/Ellie_In)\
**Replies:** 3\
**Last updated:** [May 29, 2025, 7:38pm UTC](https://discourse.slicer.org/t/morphocloud-instance-issue/42645 "2025-05-29T19:38:30Z")

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I was wondering if anyone had any experience with MorphoCloud instances and could help me figure out what is going wrong. When I try to unshelve my instance, I get an error that says “failed to associate floating IP w…

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## [Graphics processor in MorphoCloud not working?](https://discourse.slicer.org/t/graphics-processor-in-morphocloud-not-working/43027)

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**Author:** [@Dave\_Matthews](https://discourse.slicer.org/u/Dave_Matthews)\
**Replies:** 2\
**Last updated:** [May 21, 2025, 8:22pm UTC](https://discourse.slicer.org/t/graphics-processor-in-morphocloud-not-working/43027 "2025-05-21T20:22:15Z")

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I recently initiated a MorphoCloud instance (Instance-277, g3.xl) and it was working great this morning. However, this afternoon I unshelved it and tried to load in the same dataset I was working with earlier. This time…

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## [SlicerMorph - semilandmarks](https://discourse.slicer.org/t/slicermorph-semilandmarks/34331)

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**Author:** [@Katya\_Stansfield](https://discourse.slicer.org/u/Katya_Stansfield)\
**Replies:** 5\
**Last updated:** [April 23, 2025, 7:13pm UTC](https://discourse.slicer.org/t/slicermorph-semilandmarks/34331 "2025-04-23T19:13:16Z")

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Hello – may I ask for help with semilandmark projection using either Alpaca or ProjectSemiLM. I have fairly simple surface objects so that Alpaca struggles to superimpose meshes without errors. Sometime it works just fi…

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## [Using SkyScanReconImport - do I need to change my .log file?](https://discourse.slicer.org/t/using-skyscanreconimport-do-i-need-to-change-my-log-file/42644)

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**Author:** [@atay5510](https://discourse.slicer.org/u/atay5510)\
**Replies:** 2\
**Last updated:** [April 22, 2025, 8:28am UTC](https://discourse.slicer.org/t/using-skyscanreconimport-do-i-need-to-change-my-log-file/42644 "2025-04-22T08:28:10Z")

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I have scanned some specimens on a Bruker SkyScan 2214 MicroCT. I have transferred these scans into a separate computer from the machine I used to acquire the images. As such, in the .log file, the Home Directory and Da…

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## [SlicerMorph ImageStacks ROI transformation yields incorrect cropping](https://discourse.slicer.org/t/slicermorph-imagestacks-roi-transformation-yields-incorrect-cropping/42525)

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**Author:** [@scutisorex](https://discourse.slicer.org/u/scutisorex)\
**Replies:** 2\
**Last updated:** [April 10, 2025, 4:01pm UTC](https://discourse.slicer.org/t/slicermorph-imagestacks-roi-transformation-yields-incorrect-cropping/42525 "2025-04-10T16:01:15Z")

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Hi all, I’m using ImageStacks to import ROIs of some larger CT stacks. I specified my ROI using Markups and transformed it to include only the portion of the scan I wanted (skull of the animal, see below). This included…

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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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## [Converting 2d hand drawn atlas into 3d atlas with region volumes](https://discourse.slicer.org/t/converting-2d-hand-drawn-atlas-into-3d-atlas-with-region-volumes/41920)

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**Author:** [@imillercrews](https://discourse.slicer.org/u/imillercrews)\
**Replies:** 2\
**Last updated:** [March 3, 2025, 1:58pm UTC](https://discourse.slicer.org/t/converting-2d-hand-drawn-atlas-into-3d-atlas-with-region-volumes/41920 "2025-03-03T13:58:37Z")

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My field uses an old hand drawn bird brain atlas from the 70’s for doing dissections and I wanted to try and convert the 2d images into a 3d model for demonstration and training purposes. Does this seem like something 3D…

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## [Warping estimated semilandmarks onto surface](https://discourse.slicer.org/t/warping-estimated-semilandmarks-onto-surface/41354)

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**Author:** [@stineblom](https://discourse.slicer.org/u/stineblom)\
**Replies:** 8\
**Last updated:** [February 5, 2025, 1:47pm UTC](https://discourse.slicer.org/t/warping-estimated-semilandmarks-onto-surface/41354 "2025-02-05T13:47:08Z")

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Hello! Using pseudoLMgenerator and ALPACA, I have produced 499 pseudolandmarks on a sample of scapulae from different species that cover the whole surface/shape. From these, I made an ancestral shape reconstruction (ASR…

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## [SlicerMorph 3D Morphometrics short course in Sao Paulo Brazil in December](https://discourse.slicer.org/t/slicermorph-3d-morphometrics-short-course-in-sao-paulo-brazil-in-december/40063)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 0\
**Last updated:** [November 7, 2024, 4:57am UTC](https://discourse.slicer.org/t/slicermorph-3d-morphometrics-short-course-in-sao-paulo-brazil-in-december/40063 "2024-11-07T04:57:01Z")

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Thanks to funding from Sao Paulo University, we are organizing a week long short course in SlicerMorph that will cover all aspects of conducting morphological and morphometrics research on 3D data for colleagues in Brazi…

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## [VolumePropertyAction Animator Problem](https://discourse.slicer.org/t/volumepropertyaction-animator-problem/40531)

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**Author:** [@Ellie\_In](https://discourse.slicer.org/u/Ellie_In)\
**Replies:** 2\
**Last updated:** [December 5, 2024, 10:46pm UTC](https://discourse.slicer.org/t/volumepropertyaction-animator-problem/40531 "2024-12-05T22:46:56Z")

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Hello, I’m new to Slicer so I’m not sure if this issue is my fault or not, so any insight would be appreciated. I am trying to create an animation using the VolumePropertyAction and I set my start property and end prope…

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## [Merging landmarks and semi-landmarks with SlicerMorph](https://discourse.slicer.org/t/merging-landmarks-and-semi-landmarks-with-slicermorph/39977)

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**Author:** [@Ruiqi-CUB](https://discourse.slicer.org/u/Ruiqi-CUB)\
**Replies:** 9\
**Last updated:** [November 21, 2024, 5:50pm UTC](https://discourse.slicer.org/t/merging-landmarks-and-semi-landmarks-with-slicermorph/39977 "2024-11-21T17:50:48Z")

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I am Slicer 5.6.2. My project use 1) 5 homologous landmarks 2) semilandmarks on a open curve 3) semilandmarks on a closed curve, My goal is to merge them and create a PCA plot in R with merged data. I tried to use Merge…

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## [SlicerMorph MorphologikaLMConverter module- landmark orientation issue](https://discourse.slicer.org/t/slicermorph-morphologikalmconverter-module-landmark-orientation-issue/40256)

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**Author:** [@A\_Auerbach](https://discourse.slicer.org/u/A_Auerbach)\
**Replies:** 3\
**Last updated:** [November 20, 2024, 4:31pm UTC](https://discourse.slicer.org/t/slicermorph-morphologikalmconverter-module-landmark-orientation-issue/40256 "2024-11-20T16:31:11Z")

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Hello all, I’ve used Slicer for segmentation but Checkpoint for landmarking, exporting my landmarks as Morphologika and csv files. However, to create good visualizations of my landmarks on the skull surface for publicat…

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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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## [Horizontal Noise in 3D Reconstruction Using Slicer](https://discourse.slicer.org/t/horizontal-noise-in-3d-reconstruction-using-slicer/38031)

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**Author:** [@ypd04474](https://discourse.slicer.org/u/ypd04474)\
**Replies:** 2\
**Last updated:** [August 27, 2024, 8:03am UTC](https://discourse.slicer.org/t/horizontal-noise-in-3d-reconstruction-using-slicer/38031 "2024-08-27T08:03:39Z")

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I’m currently working on a 3D reconstruction project using Slicer, but I’ve encountered an issue where horizontal noise appears in the final 3D model. The source images are 2D slices, and the reconstruction generally lo…

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## [Cropping mesh using landmark points](https://discourse.slicer.org/t/cropping-mesh-using-landmark-points/16167)

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**Author:** [@DiamondKMG](https://discourse.slicer.org/u/DiamondKMG)\
**Replies:** 1\
**Last updated:** [February 23, 2021, 9:13pm UTC](https://discourse.slicer.org/t/cropping-mesh-using-landmark-points/16167 "2021-02-23T21:13:14Z")

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I used the model to model distance module to create the heat map displayed below to represent the difference between the mean shape of my sample and extreme shape at the positive end of a principal component from a Gener…

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