# SlicerSALT

**URL:** https://discourse.slicer.org/c/community/slicer-salt/14.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 SlicerSALT category](https://discourse.slicer.org/t/about-the-slicersalt-category/47)

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**Author:** [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Replies:** 1\
**Last updated:** [May 16, 2023, 2:00am UTC](https://discourse.slicer.org/t/about-the-slicersalt-category/47 "2023-05-16T02:00:22Z")

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SlicerSALT is an under development customized Slicer with the aim of consolidating the various statistical shape analysis tools in one place. You can find more information about SlicerSALT at its website. This category…

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## [Average mesh module](https://discourse.slicer.org/t/average-mesh-module/45422)

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**Author:** [@elisa](https://discourse.slicer.org/u/elisa)\
**Replies:** 0\
**Last updated:** [December 9, 2025, 3:49pm UTC](https://discourse.slicer.org/t/average-mesh-module/45422 "2025-12-09T15:49:33Z")

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Hi, I study imprints in ceramics and I want to reproduce a tool by averaging different meshes of the imprint. I used the average mesh module, selected my different meshes as inputs, creating a new model as output, but i…

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## [SlicerSALT crashes when loading data](https://discourse.slicer.org/t/slicersalt-crashes-when-loading-data/43686)

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**Author:** [@Chihiro\_Suzuki](https://discourse.slicer.org/u/Chihiro_Suzuki)\
**Replies:** 4\
**Last updated:** [August 3, 2025, 2:42pm UTC](https://discourse.slicer.org/t/slicersalt-crashes-when-loading-data/43686 "2025-08-03T14:42:55Z")

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Dear Slicer community, I am currently planning to use SHPARM to compare the morphology of mammalian paranasal sinuses. To prepare for this, I have been independently studying both SlicerSALT and the SHPARM methodology. …

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## [SPHARM PDM Correspondence improvement](https://discourse.slicer.org/t/spharm-pdm-correspondence-improvement/23897)

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**Author:** [@lili-yu22](https://discourse.slicer.org/u/lili-yu22)\
**Replies:** 23\
**Last updated:** [July 12, 2025, 8:54pm UTC](https://discourse.slicer.org/t/spharm-pdm-correspondence-improvement/23897 "2025-07-12T20:54:19Z")

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Slicer salt3.0，windows10 when I use“ spharm-pdm correspondence improvement ”the python show "OSError：Invalid argument：“C：//users//…//2022—06—16T11:51:18.762701.csv”. the input models directory: i use the\*SPHARM.vtk. …

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## [How to measure the mandibular condyle morphological changes between two time different points CT?](https://discourse.slicer.org/t/how-to-measure-the-mandibular-condyle-morphological-changes-between-two-time-different-points-ct/25677)

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**Author:** [@wael\_telha](https://discourse.slicer.org/u/wael_telha)\
**Replies:** 6\
**Last updated:** [July 12, 2025, 1:58pm UTC](https://discourse.slicer.org/t/how-to-measure-the-mandibular-condyle-morphological-changes-between-two-time-different-points-ct/25677 "2025-07-12T13:58:00Z")

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Hi 3D Slicer users, I am currently conducting a research to measure the mandibular condyle morphological changes between two time-different points CT: I tried to use SPHARM-PDM to achieve this goal but it is not workin…

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## [Population Analysis Output](https://discourse.slicer.org/t/population-analysis-output/43644)

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**Author:** [@anasmh101](https://discourse.slicer.org/u/anasmh101)\
**Replies:** 4\
**Last updated:** [July 10, 2025, 5:52pm UTC](https://discourse.slicer.org/t/population-analysis-output/43644 "2025-07-10T17:52:38Z")

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Hello everyone, I’m currently working on a project that involves analyzing bone apposition and resorption in mandibular condyles by comparing pre-treatment and post-treatment CBCT scans. Here’s what I’ve done so far: …

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## [Covariate Significance Testing - shape for p-value?](https://discourse.slicer.org/t/covariate-significance-testing-shape-for-p-value/29084)

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**Author:** [@Yuyoung](https://discourse.slicer.org/u/Yuyoung)\
**Replies:** 1\
**Last updated:** [July 8, 2025, 3:21am UTC](https://discourse.slicer.org/t/covariate-significance-testing-shape-for-p-value/29084 "2025-07-08T03:21:51Z")

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Hello everyone, I am currently using version 4.0.1 - 2023-02-08 of SlicerSALT to check out the morphological changes in the human pubic symphyseal surface as a result of aging. Specifically, I am now analyzing four age …

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## [Evolutionary S-rep fitting](https://discourse.slicer.org/t/evolutionary-s-rep-fitting/43075)

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**Author:** [@Deep\_Learning](https://discourse.slicer.org/u/Deep_Learning)\
**Replies:** 4\
**Last updated:** [June 23, 2025, 3:30pm UTC](https://discourse.slicer.org/t/evolutionary-s-rep-fitting/43075 "2025-06-23T15:30:00Z")

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Is it possible to batch this with a csv file? Or does it need to be done in python?

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## [SlicerSALT 5.0: Summary, Highlights and Changelog](https://discourse.slicer.org/t/slicersalt-5-0-summary-highlights-and-changelog/39546)

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**Author:** [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Replies:** 10\
**Last updated:** [May 21, 2025, 2:13am UTC](https://discourse.slicer.org/t/slicersalt-5-0-summary-highlights-and-changelog/39546 "2025-05-21T02:13:41Z")

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The SlicerSALT team is proud to announce that version 5.0 is now available for download. This release introduces new features as well as bug fixes for better performance and stability. This release of SlicerSALT includes…

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## [SLICER SALT .... having trouble with "Generate Shape Analysis Structure"](https://discourse.slicer.org/t/slicer-salt-having-trouble-with-generate-shape-analysis-structure/42827)

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**Author:** [@Deep\_Learning](https://discourse.slicer.org/u/Deep_Learning)\
**Replies:** 3\
**Last updated:** [May 16, 2025, 12:45pm UTC](https://discourse.slicer.org/t/slicer-salt-having-trouble-with-generate-shape-analysis-structure/42827 "2025-05-16T12:45:06Z")

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I’m having trouble with data importer, SlicerSalt 6.0.0. I can import and view the sampledata, but when I try to “Generate Shape Analysis Structure” I get this error on windows and linux. Traceback (most recent call l…

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## [SlicerSALT 6.0: Summary and Changelog](https://discourse.slicer.org/t/slicersalt-6-0-summary-and-changelog/42797)

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**Author:** [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Replies:** 0\
**Last updated:** [May 5, 2025, 12:47pm UTC](https://discourse.slicer.org/t/slicersalt-6-0-summary-and-changelog/42797 "2025-05-05T12:47:13Z")

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The SlicerSALT team is proud to announce that version 6.0 is now available for download. This release introduces new features as well as bug fixes for better performance and stability. This release of SlicerSALT includes…

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## [Covariate significance testing - What is it?](https://discourse.slicer.org/t/covariate-significance-testing-what-is-it/12118)

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**Author:** [@quentin\_devignes](https://discourse.slicer.org/u/quentin_devignes)\
**Replies:** 17\
**Last updated:** [April 4, 2025, 10:14am UTC](https://discourse.slicer.org/t/covariate-significance-testing-what-is-it/12118 "2025-04-04T10:14:18Z")

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Dear SlicerSALT team, We are analyzing parkinsonian patients with different cognitive profiles (4 groups in total) and we are interesting in studying shape deformations of subcortical structures between these groups. We…

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## [SlicerSALT tutorials are now in Read the Docs](https://discourse.slicer.org/t/slicersalt-tutorials-are-now-in-read-the-docs/42247)

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**Author:** [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Replies:** 0\
**Last updated:** [March 21, 2025, 4:13pm UTC](https://discourse.slicer.org/t/slicersalt-tutorials-are-now-in-read-the-docs/42247 "2025-03-21T16:13:28Z")

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We have finally moved all of our tutorials to ReadTheDocs. Now it is much easier for you, our SlicerSALT community, to add to the documentation of its functionality. Looking forward to your contributions!!

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## [Create average model with shapevariationanalyzer](https://discourse.slicer.org/t/create-average-model-with-shapevariationanalyzer/3581)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 10\
**Last updated:** [March 17, 2025, 3:24pm UTC](https://discourse.slicer.org/t/create-average-model-with-shapevariationanalyzer/3581 "2025-03-17T15:24:07Z")

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Slicer version:4.8.1 Hi 3D slicer experts: I want to compare the average of two group models to each other, so I use the shapevariationanalyzer module for computing the average models . It computes the mean group for m…

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## [SlicerSALT 4.0.1: Summary, Highlights and Changelog](https://discourse.slicer.org/t/slicersalt-4-0-1-summary-highlights-and-changelog/26197)

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**Author:** [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Replies:** 4\
**Last updated:** [December 21, 2024, 5:45am UTC](https://discourse.slicer.org/t/slicersalt-4-0-1-summary-highlights-and-changelog/26197 "2024-12-21T05:45:51Z")

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The SlicerSALT team is proud to announce that version 4.0.1 is now available for download. This release introduces new features as well as bug fixes for better performance and stability. The development of SlicerSALT is …

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## [PlaneCNNTrainer](https://discourse.slicer.org/t/planecnntrainer/40320)

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**Author:** [@Tom\_Bigonneau](https://discourse.slicer.org/u/Tom_Bigonneau)\
**Replies:** 0\
**Last updated:** [November 21, 2024, 10:19pm UTC](https://discourse.slicer.org/t/planecnntrainer/40320 "2024-11-21T22:19:23Z")

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Hello, I’m using the plane CNN trainer on the data obtained with the SurfacePlaneMapper. I just changed them to have the right\_\<feature\_name\>\_flat.jpeg waited. I have the V06, the good modality. I click on Start trai…

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## [Covariate Signficance Testing (MFSDA) - Variable Types?](https://discourse.slicer.org/t/covariate-signficance-testing-mfsda-variable-types/37989)

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**Author:** [@kmadi](https://discourse.slicer.org/u/kmadi)\
**Replies:** 0\
**Last updated:** [August 21, 2024, 7:42pm UTC](https://discourse.slicer.org/t/covariate-signficance-testing-mfsda-variable-types/37989 "2024-08-21T19:42:55Z")

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Hello SlicerSALT developers, community, Quick question regarding how the Covariate Significance Testing (MFSDA) module treats variables/covariates as they are listed on the input CSV: Does MFSDA distinguish between var…

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## [Normal projection vectors: meshmath.exe vs. Model-to-Model Distance](https://discourse.slicer.org/t/normal-projection-vectors-meshmath-exe-vs-model-to-model-distance/36889)

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**Author:** [@kmadi](https://discourse.slicer.org/u/kmadi)\
**Replies:** 0\
**Last updated:** [June 19, 2024, 12:59am UTC](https://discourse.slicer.org/t/normal-projection-vectors-meshmath-exe-vs-model-to-model-distance/36889 "2024-06-19T00:59:48Z")

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Hello Slicer(SALT) devs, I am revising a python script to run the Model-to-Model Distance module in CLI so I can automate the process for a large batch of VTKs. Specifically, I’m looking to extract the normal projection…

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## [Slicer SALT attribute to measure bone resorption](https://discourse.slicer.org/t/slicer-salt-attribute-to-measure-bone-resorption/33699)

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**Author:** [@anasmh101](https://discourse.slicer.org/u/anasmh101)\
**Replies:** 5\
**Last updated:** [April 29, 2024, 2:41am UTC](https://discourse.slicer.org/t/slicer-salt-attribute-to-measure-bone-resorption/33699 "2024-04-29T02:41:12Z")

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Hello everyone, may I ask which attribute in Shape population viewer represents bone resorption/deposition in mandible condyle for (pre/post treatment condyle ), I have done model to model distance ( corresponding point…

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## [registration based correspondence crashing](https://discourse.slicer.org/t/registration-based-correspondence-crashing/35716)

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**Author:** [@clairez](https://discourse.slicer.org/u/clairez)\
**Replies:** 0\
**Last updated:** [April 24, 2024, 7:41pm UTC](https://discourse.slicer.org/t/registration-based-correspondence-crashing/35716 "2024-04-24T19:41:18Z")

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Operating system: Windows Slicer version: SlicerSALT 4.0.1 -2023-09-21 Expected behavior: register bones to be corresponding Actual behavior: crashing

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## [Lumbar Spine PCA](https://discourse.slicer.org/t/lumbar-spine-pca/35170)

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**Author:** [@LeidyMoraV](https://discourse.slicer.org/u/LeidyMoraV)\
**Replies:** 3\
**Last updated:** [March 29, 2024, 8:04pm UTC](https://discourse.slicer.org/t/lumbar-spine-pca/35170 "2024-03-29T20:04:08Z")

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Hello! I’m new to Slicer and I need to use Principal Component Analysis (PCA) to get the mean shape of a dataset of L4 vertebrae, I’ve tried using SlicerSALT, and the topology of the files seem to be consistent for Circl…

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## [Exit code to terminate SPHARM-PDM upon completion in CLI?](https://discourse.slicer.org/t/exit-code-to-terminate-spharm-pdm-upon-completion-in-cli/34803)

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**Author:** [@kmadi](https://discourse.slicer.org/u/kmadi)\
**Replies:** 0\
**Last updated:** [March 9, 2024, 5:20pm UTC](https://discourse.slicer.org/t/exit-code-to-terminate-spharm-pdm-upon-completion-in-cli/34803 "2024-03-09T17:20:12Z")

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Hello! I’ve spoken to a couple of the developers in person but I figured I’d ask here for a wider reach. I’m currently using a python script to execute the SPHARM-PDM module in a command line interface (CLI) via python’…

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## [SPHARM-PDM error: "Not enough points; cannot solve SPHARM coefficients."](https://discourse.slicer.org/t/spharm-pdm-error-not-enough-points-cannot-solve-spharm-coefficients/34673)

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**Author:** [@etour](https://discourse.slicer.org/u/etour)\
**Replies:** 1\
**Last updated:** [March 4, 2024, 1:01pm UTC](https://discourse.slicer.org/t/spharm-pdm-error-not-enough-points-cannot-solve-spharm-coefficients/34673 "2024-03-04T13:01:31Z")

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Hi everyone! I’ve just attempted to process 8 .nrrd files using the SPHARM ‘Shape Analysis Module’. 7 of these files have worked as expected, and I get all the right outputs at the end. However, I’m having issues with 1…

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## [SPHARM-PDM Error: 'SegPostProcess terminated with a numerical fault'](https://discourse.slicer.org/t/spharm-pdm-error-segpostprocess-terminated-with-a-numerical-fault/34519)

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**Author:** [@etour](https://discourse.slicer.org/u/etour)\
**Replies:** 6\
**Last updated:** [March 3, 2024, 12:31am UTC](https://discourse.slicer.org/t/spharm-pdm-error-segpostprocess-terminated-with-a-numerical-fault/34519 "2024-03-03T00:31:33Z")

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Hello! I’ve been attempting to use SlicerSALT SPHARM-PDM to compare the shape of some archaeological artefacts that I’m analysing (clay documents, to be more specific). My original 3D mesh files are .ply, and I’ve been a…

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## [Run shape analysis runtime indefinite](https://discourse.slicer.org/t/run-shape-analysis-runtime-indefinite/31398)

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**Author:** [@pkashya](https://discourse.slicer.org/u/pkashya)\
**Replies:** 4\
**Last updated:** [January 19, 2024, 2:08pm UTC](https://discourse.slicer.org/t/run-shape-analysis-runtime-indefinite/31398 "2024-01-19T14:08:16Z")

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Hi, I’m running the shape analysis module on a hippocampus segmentation mask (.vtk/.nii/\*.nrrd) and it does not seem to complete for some reason. I’m following the steps on the documentation (SlicerSALT-SPHARM-PDM-Tutor…

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## [PCA creation error in Population analysis module](https://discourse.slicer.org/t/pca-creation-error-in-population-analysis-module/33602)

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**Author:** [@Shoaib\_Attar](https://discourse.slicer.org/u/Shoaib_Attar)\
**Replies:** 0\
**Last updated:** [January 3, 2024, 3:01pm UTC](https://discourse.slicer.org/t/pca-creation-error-in-population-analysis-module/33602 "2024-01-03T15:01:54Z")

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I am trying to create a PCA chart with a set of 4 femurs and I keep getting the error as shown in the picture. THe same dataset is working in Shapeworks software but it doesn’t work here. Can anyone please help me sol…

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## ["Not Responding" error in 'Shape Population Viewer' extension for Slicer 5.2.2 version ](https://discourse.slicer.org/t/not-responding-error-in-shape-population-viewer-extension-for-slicer-5-2-2-version/29877)

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**Author:** [@Solayman](https://discourse.slicer.org/u/Solayman)\
**Replies:** 1\
**Last updated:** [August 22, 2023, 10:42am UTC](https://discourse.slicer.org/t/not-responding-error-in-shape-population-viewer-extension-for-slicer-5-2-2-version/29877 "2023-08-22T10:42:16Z")

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I am facing an error in the ‘Shape Population Viewer’ extension for Slicer 5.2.2 version, However, I didn’t face that ‘Not Responding’ error. Could anyone help me?

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## [Aligned SPHARM models flip inside out during PCA](https://discourse.slicer.org/t/aligned-spharm-models-flip-inside-out-during-pca/30768)

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**Author:** [@ayersmanmal](https://discourse.slicer.org/u/ayersmanmal)\
**Replies:** 0\
**Last updated:** [July 25, 2023, 12:58am UTC](https://discourse.slicer.org/t/aligned-spharm-models-flip-inside-out-during-pca/30768 "2023-07-25T00:58:16Z")

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Operating system: Windows Slicer version: 4.0.1 After following through with the shape population analysis module, the resultant PCA output has the models turning inside out. Since the three SPHARM.vtk files that make …

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## [Shape analysis by SPHARM-PDM](https://discourse.slicer.org/t/shape-analysis-by-spharm-pdm/1708)

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**Author:** [@sodaGH](https://discourse.slicer.org/u/sodaGH)\
**Replies:** 8\
**Last updated:** [May 2, 2023, 7:17pm UTC](https://discourse.slicer.org/t/shape-analysis-by-spharm-pdm/1708 "2023-05-02T19:17:43Z")

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Operating system: windows7\_64 Slicer version: 4.4.0 Expected behavior: I want to do the shape analysis by SPHARM-PDM Actual behavior: I have apply the shape analysis module, when I load the output.csv file in ShapeP…

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## [Covariate Significance testing - Pvalues always equals to 1](https://discourse.slicer.org/t/covariate-significance-testing-pvalues-always-equals-to-1/28975)

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**Author:** [@Giulia\_Baldassari](https://discourse.slicer.org/u/Giulia_Baldassari)\
**Replies:** 0\
**Last updated:** [April 17, 2023, 5:52pm UTC](https://discourse.slicer.org/t/covariate-significance-testing-pvalues-always-equals-to-1/28975 "2023-04-17T17:52:46Z")

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Dear experts, I used SlicerSalt software to carry out a shape analysis but whichever database I used and for different substructures such as caudate, hippocampus and amygdala the pvalue was always non-significant. In pa…

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