# SlicerMorph

**URL:** https://discourse.slicer.org/c/community/biological-morphology-slicer-extension/24.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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## [About the SlicerMorph category](https://discourse.slicer.org/t/about-the-slicermorph-category/9631)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 0

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## [PCA visualization parameters](https://discourse.slicer.org/t/pca-visualization-parameters/47141)

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**Author:** [@Stephan\_Collins](https://discourse.slicer.org/u/Stephan_Collins)\
**Replies:** 5\
**Last updated:** [May 27, 2026, 4:14pm UTC](https://discourse.slicer.org/t/pca-visualization-parameters/47141 "2026-05-27T16:14:55Z")

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Hi everyone, I am working with the GPA module from slicermorph and I noticed some changes which are most likely intentional and for good reasons but I need to ask. When you have a PCA showing segregation thanks to mult…

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## [DECA mean shape model: partly coarse surface](https://discourse.slicer.org/t/deca-mean-shape-model-partly-coarse-surface/46332)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 8\
**Last updated:** [March 16, 2026, 4:02pm UTC](https://discourse.slicer.org/t/deca-mean-shape-model-partly-coarse-surface/46332 "2026-03-16T16:02:33Z")

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Hi, I am using DECA for some shape analysis. I am wondering why the resulting reference / atlas shape model appears to have partly coarse surface. The workflow for comparing 2 groups looks like this: first: using …

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## [DECA --\> any requirements on decimation of the model?](https://discourse.slicer.org/t/deca-any-requirements-on-decimation-of-the-model/46282)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 1\
**Last updated:** [February 25, 2026, 4:16pm UTC](https://discourse.slicer.org/t/deca-any-requirements-on-decimation-of-the-model/46282 "2026-02-25T16:16:46Z")

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Hi, I am wondering if there are any recommandations for decimation of the 3D model of interest. Working with CT data of mouse skull, the original 3D ply model is about 100 MB. After running “quadratic” decimation wit…

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## [Deformable model registration prototype](https://discourse.slicer.org/t/deformable-model-registration-prototype/45426)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 0\
**Last updated:** [December 9, 2025, 5:47pm UTC](https://discourse.slicer.org/t/deformable-model-registration-prototype/45426 "2025-12-09T17:47:32Z")

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I have enabled deformable model registration as fourth level of registration (scaling, rigid, affine) in FastModelAlign module of SlicerMorph extension. Like ALPACA, it uses the point cloud based registration via Coheren…

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## [How Can I Exclude Teeth When Creating Semi-Landmarks on the Mandible?](https://discourse.slicer.org/t/how-can-i-exclude-teeth-when-creating-semi-landmarks-on-the-mandible/45222)

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**Author:** [@Esra\_Karacan](https://discourse.slicer.org/u/Esra_Karacan)\
**Replies:** 1\
**Last updated:** [November 25, 2025, 6:00pm UTC](https://discourse.slicer.org/t/how-can-i-exclude-teeth-when-creating-semi-landmarks-on-the-mandible/45222 "2025-11-25T18:00:26Z")

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Dear all, I am working on human mandibles. Most of my material has missing teeth. So, I would like to discard the teeth and put the semi-landmarks on just bone. I tried to delete the teeth, but the software put on the s…

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## [DeCAL & DeCA —\> option for selecting sample basis for reference shape](https://discourse.slicer.org/t/decal-deca-option-for-selecting-sample-basis-for-reference-shape/45075)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 2\
**Last updated:** [November 17, 2025, 3:38pm UTC](https://discourse.slicer.org/t/decal-deca-option-for-selecting-sample-basis-for-reference-shape/45075 "2025-11-17T15:38:12Z")

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Dear SlicerMorph team, would it be possible to add an additional option for the generation of the “mean shape”? For my work, probably for other users too, it would be very useful to be able to choose which shapes should…

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## [Fcsv Landmark Verileri ile Grup Bazlı PCA](https://discourse.slicer.org/t/fcsv-landmark-verileri-ile-grup-bazli-pca/44949)

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**Author:** [@Esra\_Karacan](https://discourse.slicer.org/u/Esra_Karacan)\
**Replies:** 1\
**Last updated:** [November 3, 2025, 4:35pm UTC](https://discourse.slicer.org/t/fcsv-landmark-verileri-ile-grup-bazli-pca/44949 "2025-11-03T16:35:46Z")

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Hello, I am comparing my archaeological and modern mandible data. I saved my landmark sets in fcsv format. I would like to include male and female individuals as separate groups for PCA analysis. Could you guide me on h…

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## [DeCAL & DeCA ---\> store / export applied transformations too?](https://discourse.slicer.org/t/decal-deca-store-export-applied-transformations-too/44845)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 1\
**Last updated:** [October 22, 2025, 3:22pm UTC](https://discourse.slicer.org/t/decal-deca-store-export-applied-transformations-too/44845 "2025-10-22T15:22:06Z")

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Dear SlicerMorph team, would it be possible to store / export the applied transformation too? DeCAL / DeCA algorithm is already computing : 3D models are registered to the mean of the 3D models of interest. Hence,the i…

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## [Applying semi-landmarks obtained with PseudoLMGenerator to other models](https://discourse.slicer.org/t/applying-semi-landmarks-obtained-with-pseudolmgenerator-to-other-models/44783)

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**Author:** [@BerfinSuYlcnts](https://discourse.slicer.org/u/BerfinSuYlcnts)\
**Replies:** 1\
**Last updated:** [October 16, 2025, 3:24pm UTC](https://discourse.slicer.org/t/applying-semi-landmarks-obtained-with-pseudolmgenerator-to-other-models/44783 "2025-10-16T15:24:42Z")

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Hello, I successfully completed the semi-landmark acquisition process on a sample model using the PseudoLMGenerator plugin. However, I only performed it for one sample. Now, I want to apply the same number and equally …

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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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## [ALPACA (MALPACA) TUTORIAL: K-means\_templates\_selection](https://discourse.slicer.org/t/alpaca-malpaca-tutorial-k-means-templates-selection/43204)

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**Author:** [@Nicola\_Calcabrini](https://discourse.slicer.org/u/Nicola_Calcabrini)\
**Replies:** 1\
**Last updated:** [June 3, 2025, 2:37pm UTC](https://discourse.slicer.org/t/alpaca-malpaca-tutorial-k-means-templates-selection/43204 "2025-06-03T14:37:39Z")

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good morning, I’m trying the alpaca tutorial from this link: "https://github.com/chz31/Tutorials/blob/main/MALPACA/K-means\_templates\_selection.md " unfortunately I can’t get past the second step, I attach screenshot to …

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## [Landmarking/Semi-Landmarking Query](https://discourse.slicer.org/t/landmarking-semi-landmarking-query/42690)

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**Author:** [@elg67](https://discourse.slicer.org/u/elg67)\
**Replies:** 1\
**Last updated:** [April 25, 2025, 4:31pm UTC](https://discourse.slicer.org/t/landmarking-semi-landmarking-query/42690 "2025-04-25T16:31:52Z")

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Hiya! I’m currently trying to place landmarks on crania, scapulae, clavicles and pelvises to analyse co-variation in shape. I’ve placed landmarks manually on all samples and have started creating semi-landmarks be…

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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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## [3D slicer for confocal microscopy Z stack tiffs](https://discourse.slicer.org/t/3d-slicer-for-confocal-microscopy-z-stack-tiffs/42449)

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**Author:** [@Aro\_Nugawela](https://discourse.slicer.org/u/Aro_Nugawela)\
**Replies:** 1\
**Last updated:** [April 6, 2025, 2:38am UTC](https://discourse.slicer.org/t/3d-slicer-for-confocal-microscopy-z-stack-tiffs/42449 "2025-04-06T02:38:41Z")

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Sorry if I’ve posted in the wrong community/thread this is my first time on this forum. I have a series of confocal scanning sections across a 3D tissue models. Encoded into the metadata is the scaling of the images (x=…

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## [Cannot get mesh to show in interactive PC warps](https://discourse.slicer.org/t/cannot-get-mesh-to-show-in-interactive-pc-warps/42241)

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**Author:** [@christyhipsley](https://discourse.slicer.org/u/christyhipsley)\
**Replies:** 1\
**Last updated:** [March 21, 2025, 3:54am UTC](https://discourse.slicer.org/t/cannot-get-mesh-to-show-in-interactive-pc-warps/42241 "2025-03-21T03:54:57Z")

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Hi all, I’m fairly new to Slicer so forgive me if I’m missing something obvious. I loaded a previous GPA/PCA from geomorph into SlicerMorph, and everything looks fine. I can view the PC scatter plots, lollipop plots, an…

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## [Importing covariates with "Load GPA + PCA  Analysis from File"?](https://discourse.slicer.org/t/importing-covariates-with-load-gpa-pca-analysis-from-file/42118)

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**Author:** [@christyhipsley](https://discourse.slicer.org/u/christyhipsley)\
**Replies:** 1\
**Last updated:** [March 14, 2025, 1:05am UTC](https://discourse.slicer.org/t/importing-covariates-with-load-gpa-pca-analysis-from-file/42118 "2025-03-14T01:05:46Z")

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Hi all. I used the geomorph2slicermorph2 command in the SlicerMorphR package to load the results of a gpa and pca with sliding landmarks from geomorph into 3D Slicer. I would like to use some of the visualisation options…

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## [ALPACA problem: ModuleNotFoundError: No module named 'itk'](https://discourse.slicer.org/t/alpaca-problem-modulenotfounderror-no-module-named-itk/41335)

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**Author:** [@nightmare](https://discourse.slicer.org/u/nightmare)\
**Replies:** 5\
**Last updated:** [February 7, 2025, 1:46pm UTC](https://discourse.slicer.org/t/alpaca-problem-modulenotfounderror-no-module-named-itk/41335 "2025-02-07T13:46:11Z")

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Hi, how can I solve this problem? alpaca does not descend and does not open. Traceback (most recent call last): File “C:/Users/İhsanBeratKILIÇLI/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/Slicer…

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## [CreateSemiLMPatches CSV Landmark into a Single File](https://discourse.slicer.org/t/createsemilmpatches-csv-landmark-into-a-single-file/41513)

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**Author:** [@Esra\_Karacan](https://discourse.slicer.org/u/Esra_Karacan)\
**Replies:** 4\
**Last updated:** [February 6, 2025, 12:25am UTC](https://discourse.slicer.org/t/createsemilmpatches-csv-landmark-into-a-single-file/41513 "2025-02-06T00:25:45Z")

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Operating system:Windows 10 Slicer version:5.6.2 Expected behavior: I am facing technical problems in the process of converting the selected landmarks into a single file using the ‘CreateSemiLMPatches’ module in the pr…

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## [Trouble with CreateSemiLMPatches ](https://discourse.slicer.org/t/trouble-with-createsemilmpatches/40172)

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**Author:** [@rkempston](https://discourse.slicer.org/u/rkempston)\
**Replies:** 1\
**Last updated:** [November 13, 2024, 4:34pm UTC](https://discourse.slicer.org/t/trouble-with-createsemilmpatches/40172 "2024-11-13T16:34:23Z")

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Hi all, I just wanted to clarify something, when creating semilandmark patches, are you limited to the first 100 markup points to define the semilandmark grid points? As I can only enter grid points up to 100.

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## [Sliding semilandmarks](https://discourse.slicer.org/t/sliding-semilandmarks/39828)

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**Author:** [@Logan\_Moore](https://discourse.slicer.org/u/Logan_Moore)\
**Replies:** 9\
**Last updated:** [October 29, 2024, 4:55am UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828 "2024-10-29T04:55:25Z")

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Hi guys, I hope you are well, I just want to make sure I am understanding the workflow of Slicermorph and SlicermorphR correctly. Apologies if this seems simple but I must have have an error somewhere and it is driving …

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## [Problem merging SemiLMPatches](https://discourse.slicer.org/t/problem-merging-semilmpatches/37971)

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**Author:** [@zifangx](https://discourse.slicer.org/u/zifangx)\
**Replies:** 4\
**Last updated:** [October 4, 2024, 3:29pm UTC](https://discourse.slicer.org/t/problem-merging-semilmpatches/37971 "2024-10-04T15:29:40Z")

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Hi, I am trying to apply surface landmarks across a region of interest in a lizard cranium, utilizing the CreateSemiLMPatches module of SlicerMorph. When I try to merge the SemiLMPatches (screenshot1) into one single nod…

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## [Trouble with PlaceSemilandmarkGrid](https://discourse.slicer.org/t/trouble-with-placesemilandmarkgrid/39531)

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**Author:** [@Sumouria](https://discourse.slicer.org/u/Sumouria)\
**Replies:** 1\
**Last updated:** [October 3, 2024, 9:09pm UTC](https://discourse.slicer.org/t/trouble-with-placesemilandmarkgrid/39531 "2024-10-03T21:09:50Z")

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Hi everybody! I’m sorting out how to place surface semilandmarks on some inner ear endocasts, in order to be able to patch a batch of them (I have 29 specimens, so I need to be able to patch rather than place each specim…

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## [When I remove the points on the crest and adjust the position of some of the points and then perform the next step“Enforce spatial sampling rate”, the software flashes back or the data in View disappear, why is that?](https://discourse.slicer.org/t/when-i-remove-the-points-on-the-crest-and-adjust-the-position-of-some-of-the-points-and-then-perform-the-next-step-enforce-spatial-sampling-rate-the-software-flashes-back-or-the-data-in-view-disappear-why-is-that/39521)

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**Author:** [@yijie3091](https://discourse.slicer.org/u/yijie3091)\
**Replies:** 1\
**Last updated:** [October 3, 2024, 5:43pm UTC](https://discourse.slicer.org/t/when-i-remove-the-points-on-the-crest-and-adjust-the-position-of-some-of-the-points-and-then-perform-the-next-step-enforce-spatial-sampling-rate-the-software-flashes-back-or-the-data-in-view-disappear-why-is-that/39521 "2024-10-03T17:43:16Z")

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Off topic, is it possible to manually adjust the position of the points when performing in the “pseudoLMgenerator”?

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## [Why is there such a large difference in the number of pseudo-landmarks projected to the ascending branches on either side? What can be done to solve this problem?](https://discourse.slicer.org/t/why-is-there-such-a-large-difference-in-the-number-of-pseudo-landmarks-projected-to-the-ascending-branches-on-either-side-what-can-be-done-to-solve-this-problem/39519)

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**Author:** [@yijie3091](https://discourse.slicer.org/u/yijie3091)\
**Replies:** 1\
**Last updated:** [October 3, 2024, 5:14pm UTC](https://discourse.slicer.org/t/why-is-there-such-a-large-difference-in-the-number-of-pseudo-landmarks-projected-to-the-ascending-branches-on-either-side-what-can-be-done-to-solve-this-problem/39519 "2024-10-03T17:14:23Z")

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## [How to make a "mandible template"from many mandibles in slicermorph?](https://discourse.slicer.org/t/how-to-make-a-mandible-template-from-many-mandibles-in-slicermorph/38241)

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**Author:** [@yijie3091](https://discourse.slicer.org/u/yijie3091)\
**Replies:** 7\
**Last updated:** [September 15, 2024, 5:04pm UTC](https://discourse.slicer.org/t/how-to-make-a-mandible-template-from-many-mandibles-in-slicermorph/38241 "2024-09-15T17:04:25Z")

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How to make a "mandible template"from many mandibles in slicermorph to match others?

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## [How can I segment crestal area precisely apart from mandible because of its variability?](https://discourse.slicer.org/t/how-can-i-segment-crestal-area-precisely-apart-from-mandible-because-of-its-variability/38242)

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**Author:** [@yijie3091](https://discourse.slicer.org/u/yijie3091)\
**Replies:** 3\
**Last updated:** [September 6, 2024, 4:35pm UTC](https://discourse.slicer.org/t/how-can-i-segment-crestal-area-precisely-apart-from-mandible-because-of-its-variability/38242 "2024-09-06T16:35:12Z")

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Because of the crestal area’s variability,how can I segment it precisely apart from mandible in slicermorph?

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## [Fix for \`no package called pandas\` in SlicerMorph ALPACA k-means template selection - Apple ARM](https://discourse.slicer.org/t/fix-for-no-package-called-pandas-in-slicermorph-alpaca-k-means-template-selection-apple-arm/36094)

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**Author:** [@jnations](https://discourse.slicer.org/u/jnations)\
**Replies:** 3\
**Last updated:** [May 12, 2024, 8:11pm UTC](https://discourse.slicer.org/t/fix-for-no-package-called-pandas-in-slicermorph-alpaca-k-means-template-selection-apple-arm/36094 "2024-05-12T20:11:36Z")

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Hi community, I’ve run into a problem with k-means template selection on 2 different mac machines. One is a 2020 MacBook Pro M1, and the second is a 2023 MacBook Pro M3 Max. Working through the tutorial here, I can run …

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## [How to reconstruct the whole vertebrae using the reconstructed volume](https://discourse.slicer.org/t/how-to-reconstruct-the-whole-vertebrae-using-the-reconstructed-volume/35463)

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**Author:** [@LeidyMoraV](https://discourse.slicer.org/u/LeidyMoraV)\
**Replies:** 6\
**Last updated:** [April 24, 2024, 5:39pm UTC](https://discourse.slicer.org/t/how-to-reconstruct-the-whole-vertebrae-using-the-reconstructed-volume/35463 "2024-04-24T17:39:35Z")

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Hello everyone, I am currently involved in a project aiming to reconstruct the complete volume of vertebrae solely from ultrasound images, specifically focusing on the posterior aspect. Our approach involves utilizing P…

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## [Digitizing semilandmarks ](https://discourse.slicer.org/t/digitizing-semilandmarks/32355)

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**Author:** [@codyprang](https://discourse.slicer.org/u/codyprang)\
**Replies:** 14\
**Last updated:** [January 10, 2024, 4:52pm UTC](https://discourse.slicer.org/t/digitizing-semilandmarks/32355 "2024-01-10T16:52:31Z")

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Hello, Does anyone know if there is a way to digitize equally spaced semilandmarks over (and constrained by) a selected area of a surface mesh? In other words, can I ‘paint’ or ‘highlight’ the faces of a surface mesh ov…

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