# SlicerMorph

**URL:** https://discourse.slicer.org/c/community/biological-morphology-slicer-extension/24.md?page=1

[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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## [Measuring Organ Volume](https://discourse.slicer.org/t/measuring-organ-volume/31836)

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**Author:** [@Hannah\_Osland](https://discourse.slicer.org/u/Hannah_Osland)\
**Replies:** 1\
**Last updated:** [September 21, 2023, 9:13pm UTC](https://discourse.slicer.org/t/measuring-organ-volume/31836 "2023-09-21T21:13:48Z")

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I have a bunch of .tif files of the entire body of an organism. I want to measure the volume of an organ in the animal. What steps should I take?

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## [Slicermorph - How to import external factor table](https://discourse.slicer.org/t/slicermorph-how-to-import-external-factor-table/31451)

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**Author:** [@Ale](https://discourse.slicer.org/u/Ale)\
**Replies:** 1\
**Last updated:** [August 30, 2023, 7:52pm UTC](https://discourse.slicer.org/t/slicermorph-how-to-import-external-factor-table/31451 "2023-08-30T19:52:46Z")

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Hi all, I’m using the GPA module of Slicermorph to visualize shape change in a PCA plot. Is the a way to build externally and import a table with different factors for use with the GPA plot options? I imported a tsv tabl…

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## [ALPACA + Bilateral Symmetry](https://discourse.slicer.org/t/alpaca-bilateral-symmetry/31029)

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**Author:** [@AaronHardgrave](https://discourse.slicer.org/u/AaronHardgrave)\
**Replies:** 4\
**Last updated:** [August 7, 2023, 8:59pm UTC](https://discourse.slicer.org/t/alpaca-bilateral-symmetry/31029 "2023-08-07T20:59:56Z")

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I am using Geometric Morphometrics to discern differences across life stages of a single species. I used PseudoLMGenerator with a plane down the center of my vertebra and used ALPACA to transfer landmarks across specimen…

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## [3d morphometry in Version 5.1](https://discourse.slicer.org/t/3d-morphometry-in-version-5-1/25674)

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**Author:** [@juliangallaun](https://discourse.slicer.org/u/juliangallaun)\
**Replies:** 5\
**Last updated:** [July 14, 2023, 4:47pm UTC](https://discourse.slicer.org/t/3d-morphometry-in-version-5-1/25674 "2023-07-14T16:47:01Z")

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Hi everyone, I have a rather general question, what version of 3DSlicer (4 or 5) would be preferable for 3d morphological analysis using landmarks? I saw that version 4 had an extension called SlicerMorph which is missi…

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## [Turn 2d image slices into 3d model](https://discourse.slicer.org/t/turn-2d-image-slices-into-3d-model/28191)

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**Author:** [@ayman\_bali](https://discourse.slicer.org/u/ayman_bali)\
**Replies:** 16\
**Last updated:** [June 21, 2023, 5:34pm UTC](https://discourse.slicer.org/t/turn-2d-image-slices-into-3d-model/28191 "2023-06-21T17:34:34Z")

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Dear community, i am new to 3d slicer and i have a set of image slices (2D), which are from a probe cut in 100 um steps, and i want to put these images together and do a 3d model. What steps do I need to follow to creat…

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## [Wish list: parallelize ALPACA / MALPACA registration](https://discourse.slicer.org/t/wish-list-parallelize-alpaca-malpaca-registration/28030)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 4\
**Last updated:** [March 1, 2023, 1:08pm UTC](https://discourse.slicer.org/t/wish-list-parallelize-alpaca-malpaca-registration/28030 "2023-03-01T13:08:25Z")

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Dear slicerMorph developers, might it be possible to consider parallelizing the MALPACA registration process? e.g. run the registration process for each template and the target mesh set in parallel. -\> 4 template…

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## [How to improve the accuracy of ALPACA @slicerMorph?](https://discourse.slicer.org/t/how-to-improve-the-accuracy-of-alpaca-slicermorph/25262)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 5\
**Last updated:** [September 19, 2022, 3:40pm UTC](https://discourse.slicer.org/t/how-to-improve-the-accuracy-of-alpaca-slicermorph/25262 "2022-09-19T15:40:19Z")

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Hi, the following experiment was performed in order to “validate” the accuracy of slicerMorph/ALPACA. 2 skull samples were measured on CT 9 landmarks were manually placed on each of the two samples experiment #…

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## [ProjectSemiLM producing file with same landmark coordinates for 78 surface landmarks](https://discourse.slicer.org/t/projectsemilm-producing-file-with-same-landmark-coordinates-for-78-surface-landmarks/25275)

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**Author:** [@Corinthia\_Black](https://discourse.slicer.org/u/Corinthia_Black)\
**Replies:** 7\
**Last updated:** [September 15, 2022, 5:57pm UTC](https://discourse.slicer.org/t/projectsemilm-producing-file-with-same-landmark-coordinates-for-78-surface-landmarks/25275 "2022-09-15T17:57:48Z")

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I am trying to produce surface landmarks on an extremely variable sclarite (hard bits of spiders/insects); however, when I run ProjectSemiLM, the data that is being generated seems to overwrite each line with the same in…

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## [Exporting H.264 or Mpeg-4 or even animated GIF after I animated with SlicerMorph.](https://discourse.slicer.org/t/exporting-h-264-or-mpeg-4-or-even-animated-gif-after-i-animated-with-slicermorph/23805)

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**Author:** [@Fullcalf42](https://discourse.slicer.org/u/Fullcalf42)\
**Replies:** 2\
**Last updated:** [June 15, 2022, 2:38am UTC](https://discourse.slicer.org/t/exporting-h-264-or-mpeg-4-or-even-animated-gif-after-i-animated-with-slicermorph/23805 "2022-06-15T02:38:34Z")

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I want to export any footage possible now that I’ve completed a SlicerMorph animation moving through a thorax in the axial plane to reveal a pulmonary embolism. It appears to export just fine but there is no file where I…

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## [Importing PC scores in 3D slicer](https://discourse.slicer.org/t/importing-pc-scores-in-3d-slicer/23671)

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**Author:** [@NoemiH](https://discourse.slicer.org/u/NoemiH)\
**Replies:** 2\
**Last updated:** [June 1, 2022, 3:46pm UTC](https://discourse.slicer.org/t/importing-pc-scores-in-3d-slicer/23671 "2022-06-01T15:46:52Z")

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Hi, I have run a PCA in MorphoJ and exported the PC scores for each individual. Is it possible to import the PC scores in 3D slicer to visualise 3D shape changes along the PC axes? I know that 3D slicer can now perform…

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## [slicerMorph - ALPACA registration error in open3d](https://discourse.slicer.org/t/slicermorph-alpaca-registration-error-in-open3d/22908)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 5\
**Last updated:** [April 13, 2022, 1:53pm UTC](https://discourse.slicer.org/t/slicermorph-alpaca-registration-error-in-open3d/22908 "2022-04-13T13:53:04Z")

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Operating system: Windows 10 Slicer version: 4.11.20210226 r29738 / 7a593c8 Expected behavior: I am trying to redo an example of the SlicerMORPH workshop (S\_2020/README.md at master · SlicerMorph/S\_2020 · GitHub). Dat…

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## [Something wrong with my ProjectSemiLM](https://discourse.slicer.org/t/something-wrong-with-my-projectsemilm/22608)

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**Author:** [@yyl](https://discourse.slicer.org/u/yyl)\
**Replies:** 6\
**Last updated:** [March 24, 2022, 2:06pm UTC](https://discourse.slicer.org/t/something-wrong-with-my-projectsemilm/22608 "2022-03-24T14:06:52Z")

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4.11 windows10 I use ProjectSemiLM to transfer semilandmarks across samples.I have existing manual landmarks on each model and use the PseudoLMGenerator to set surface semilandmarks by generating pseudo-landmarks for…

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## [ALPACA point cloud ](https://discourse.slicer.org/t/alpaca-point-cloud/22553)

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**Author:** [@carterrt](https://discourse.slicer.org/u/carterrt)\
**Replies:** 1\
**Last updated:** [March 17, 2022, 10:18am UTC](https://discourse.slicer.org/t/alpaca-point-cloud/22553 "2022-03-17T10:18:30Z")

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When using ALPACA to place a point cloud on a bone model. Is it safe to assume that no landmarks will be placed on the surfaces of the internal cavities and spongy bone? I am only looking to analyze external bone shape, …

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## [Why are my semi-landmarks not uniformly distributed?](https://discourse.slicer.org/t/why-are-my-semi-landmarks-not-uniformly-distributed/22454)

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**Author:** [@yyl](https://discourse.slicer.org/u/yyl)\
**Replies:** 5\
**Last updated:** [March 16, 2022, 6:45pm UTC](https://discourse.slicer.org/t/why-are-my-semi-landmarks-not-uniformly-distributed/22454 "2022-03-16T18:45:15Z")

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version 4.11 i use the creatsemiLMpatches to generate semi-landmarks,Is there any way to make the semi-landmarks distribution on the surface more uniform? thank you very much!!!

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## [How to obtain SlicerMorph?](https://discourse.slicer.org/t/how-to-obtain-slicermorph/18903)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 4\
**Last updated:** [March 12, 2022, 6:16am UTC](https://discourse.slicer.org/t/how-to-obtain-slicermorph/18903 "2022-03-12T06:16:32Z")

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Please follow the instructions at the official repository. We advise using the latest stable version of 3D Slicer with SlicerMorph, as updating SlicerMorph is much simpler that way. If you opt to use a preview release, …

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## [How to select an entire region from the slice](https://discourse.slicer.org/t/how-to-select-an-entire-region-from-the-slice/21092)

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**Author:** [@YihangZhao](https://discourse.slicer.org/u/YihangZhao)\
**Replies:** 7\
**Last updated:** [December 23, 2021, 9:25pm UTC](https://discourse.slicer.org/t/how-to-select-an-entire-region-from-the-slice/21092 "2021-12-23T21:25:53Z")

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I tried to reconstruct endocast of species but I don’t know how can I select the region that is correspond to the endocast. I know I can select the endocast region for each slice by manually paint it, but that is time-co…

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## [SlicerMorph: about values in sliders for PCA deformation](https://discourse.slicer.org/t/slicermorph-about-values-in-sliders-for-pca-deformation/19858)

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**Author:** [@Ale](https://discourse.slicer.org/u/Ale)\
**Replies:** 1\
**Last updated:** [September 26, 2021, 4:57am UTC](https://discourse.slicer.org/t/slicermorph-about-values-in-sliders-for-pca-deformation/19858 "2021-09-26T04:57:29Z")

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Dear Slicer community. I’m playing with GPA module, specially deforming the mean shape along principal axes. My question is if the values in the slider represent the position in percentage of the target shape? I guess t…

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## [ALPACA algorithm, and projection difficulties](https://discourse.slicer.org/t/alpaca-algorithm-and-projection-difficulties/18231)

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**Author:** [@Alex\_Tinius](https://discourse.slicer.org/u/Alex_Tinius)\
**Replies:** 6\
**Last updated:** [June 20, 2021, 7:58pm UTC](https://discourse.slicer.org/t/alpaca-algorithm-and-projection-difficulties/18231 "2021-06-20T19:58:19Z")

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I would like to use the semi-automated landmarking approach ALPACA to auto-landmark clavicles. However, I seem to be unable to find suitable parameters for the auto-landmarking process, and I was hoping you could point …

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