# SlicerSALT

**URL:** https://discourse.slicer.org/c/community/slicer-salt/14.md?page=2

[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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## [SlicerSALT 3.0 Release: Summary and Changelog](https://discourse.slicer.org/t/slicersalt-3-0-release-summary-and-changelog/12748)

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**Author:** [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Replies:** 0\
**Last updated:** [July 27, 2020, 1:39pm UTC](https://discourse.slicer.org/t/slicersalt-3-0-release-summary-and-changelog/12748 "2020-07-27T13:39:16Z")

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The SlicerSALT team is proud to announce that version 3.0 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 su…

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## [Shape analysis interpretation](https://discourse.slicer.org/t/shape-analysis-interpretation/12193)

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**Author:** [@quentin\_devignes](https://discourse.slicer.org/u/quentin_devignes)\
**Replies:** 1\
**Last updated:** [July 6, 2020, 4:12pm UTC](https://discourse.slicer.org/t/shape-analysis-interpretation/12193 "2020-07-06T16:12:44Z")

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Dear SlicerSALT team, Currently using SPHARM-PDM analysis, I wonder what interpretation could be given when there are surface differences between two groups but no volume differences (assessed with 2 different methods)…

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## [Equation for medial axis from SPHARM-PDM](https://discourse.slicer.org/t/equation-for-medial-axis-from-spharm-pdm/12311)

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**Author:** [@christinah](https://discourse.slicer.org/u/christinah)\
**Replies:** 4\
**Last updated:** [July 6, 2020, 1:58pm UTC](https://discourse.slicer.org/t/equation-for-medial-axis-from-spharm-pdm/12311 "2020-07-06T13:58:59Z")

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Operating system: MacOS Catalina Slicer version: 4.10.2 Hi there, I’ve been using SPHARM-PDM and first want to say a really, truly huge thank you – both for the tool and for the extremely helpful Google slide tutorial…

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## [Multiple labels](https://discourse.slicer.org/t/multiple-labels/4505)

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**Author:** [@gpolier](https://discourse.slicer.org/u/gpolier)\
**Replies:** 0\
**Last updated:** [October 23, 2018, 3:05pm UTC](https://discourse.slicer.org/t/multiple-labels/4505 "2018-10-23T15:05:03Z")

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Operating system:MacOs Slicer version:1.0.0 Expected behavior:generate SPHARM from multiple labels Actual behavior: Hi, I would like to create one SPHARM-model from multiple lables (Hippocampus, 3 lables for head, b…

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## [Covariate Significance Testing HELP](https://discourse.slicer.org/t/covariate-significance-testing-help/11318)

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**Author:** [@Lyndon\_Pardo](https://discourse.slicer.org/u/Lyndon_Pardo)\
**Replies:** 3\
**Last updated:** [May 2, 2020, 3:59pm UTC](https://discourse.slicer.org/t/covariate-significance-testing-help/11318 "2020-05-02T15:59:06Z")

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I am new to slicer SALT and I was trying to run this feature using sample data from Kitware Data What do I input in shape for p-values? I’m using version 2.3.0-2020-04-06. Also, when I try to select any random VTK file…

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## [Question on .coef output file](https://discourse.slicer.org/t/question-on-coef-output-file/10979)

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**Author:** [@hcc](https://discourse.slicer.org/u/hcc)\
**Replies:** 4\
**Last updated:** [April 27, 2020, 7:54pm UTC](https://discourse.slicer.org/t/question-on-coef-output-file/10979 "2020-04-27T19:54:39Z")

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Hello, Really like the SPHARM-PDM tool, and thanks in advance for your time with this query. I have the .coef file of coefficients, but it seems that they only contain coefficients for positive and zero m values. For e…

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## [Regression slicer SALT](https://discourse.slicer.org/t/regression-slicer-salt/10263)

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**Author:** [@JON](https://discourse.slicer.org/u/JON)\
**Replies:** 1\
**Last updated:** [March 5, 2020, 5:54pm UTC](https://discourse.slicer.org/t/regression-slicer-salt/10263 "2020-03-05T17:54:10Z")

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Hi @bpaniagua and others, I have a question regarding the regression tool in slicer SALT. I have longitudinal data (2 timepoints) for a group of patients and controls. I want to see where and how much (and also prefera…

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## [Skeletal representation](https://discourse.slicer.org/t/skeletal-representation/10478)

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**Author:** [@Dyatsen](https://discourse.slicer.org/u/Dyatsen)\
**Replies:** 3\
**Last updated:** [March 2, 2020, 8:44pm UTC](https://discourse.slicer.org/t/skeletal-representation/10478 "2020-03-02T20:44:42Z")

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Hello. i am following the tutorial of skeletal representation (SrepModule-Tutorial\_v5.0 - Google Slides). But there is SkeletalRepresentationRefiner in the tutorial: and i just can find Initializer and Visualizer in …

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## [SlicerSALT Community Survey](https://discourse.slicer.org/t/slicersalt-community-survey/8962)

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**Author:** [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Replies:** 1\
**Last updated:** [January 27, 2020, 1:42pm UTC](https://discourse.slicer.org/t/slicersalt-community-survey/8962 "2020-01-27T13:42:19Z")

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Dear SlicerSALT community The SlicerSALT team is making plans for the continued growth and maintenance of this toolkit. One of the main components of the plan is to seek renewal of the government funding that makes our …

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## [How to skip alignments during para to spharm mesh](https://discourse.slicer.org/t/how-to-skip-alignments-during-para-to-spharm-mesh/9848)

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**Author:** [@Oh\_jeongseok](https://discourse.slicer.org/u/Oh_jeongseok)\
**Replies:** 6\
**Last updated:** [January 21, 2020, 2:16pm UTC](https://discourse.slicer.org/t/how-to-skip-alignments-during-para-to-spharm-mesh/9848 "2020-01-21T14:16:58Z")

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Hello, I’m using 3D Slicer and SPHARM extentions. I tried making surface ssm with tibias. To apply this methods, I align all models before using SPHARM(picture on right). However, while SPHARM module is running, the al…

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## [How to make spharm mesh without alignments](https://discourse.slicer.org/t/how-to-make-spharm-mesh-without-alignments/9852)

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**Author:** [@Oh\_jeongseok](https://discourse.slicer.org/u/Oh_jeongseok)\
**Replies:** 0\
**Last updated:** [January 17, 2020, 1:24pm UTC](https://discourse.slicer.org/t/how-to-make-spharm-mesh-without-alignments/9852 "2020-01-17T13:24:24Z")

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Operating system: ubuntu 16.04 Slicer version: 4.10.2 Expected behavior: Actual behavior: Hello, I tried making surface ssm with tibias. To apply this methods, I align all models before using SPHARM(picture on ri…

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## [SPHARM analysis of 3D slicer](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630)

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**Author:** [@keven](https://discourse.slicer.org/u/keven)\
**Replies:** 6\
**Last updated:** [January 2, 2020, 3:00pm UTC](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630 "2020-01-02T15:00:33Z")

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Hello, experts! Recently, I want to use the 3D Slicer expansion module, SPHARM, to analyze the condylar models of the same patient in different periods. I used 3d-slicer to complete the registration and segmentation of …

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## [How to analyse CT data of lungs?](https://discourse.slicer.org/t/how-to-analyse-ct-data-of-lungs/9618)

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**Author:** [@Shahid\_Khan](https://discourse.slicer.org/u/Shahid_Khan)\
**Replies:** 0\
**Last updated:** [December 26, 2019, 5:55am UTC](https://discourse.slicer.org/t/how-to-analyse-ct-data-of-lungs/9618 "2019-12-26T05:55:01Z")

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Hey, I am Shahid Khan and I am very new to 3-d slicer(started a week ago). I want to analyze CT data of lung cancer and want to generate Ktrans and Ve maps. I have data in Scalar volume but to use T1 mapping I need it in…

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## [SPHARM-PDM command line running does not generate procalign files](https://discourse.slicer.org/t/spharm-pdm-command-line-running-does-not-generate-procalign-files/9555)

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**Author:** [@Shane\_TANG](https://discourse.slicer.org/u/Shane_TANG)\
**Replies:** 0\
**Last updated:** [December 18, 2019, 11:25pm UTC](https://discourse.slicer.org/t/spharm-pdm-command-line-running-does-not-generate-procalign-files/9555 "2019-12-18T23:25:59Z")

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Hi all, I am using command line to perform SPHARM-PDM. My command is shown below: ./SlicerSALT --no-main-window --python-script path-to-py path-to-param And I have modified the SPHARM-PDM-parameters.ini file like this…

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## [Groups tutorial - sample data / guidance?](https://discourse.slicer.org/t/groups-tutorial-sample-data-guidance/6375)

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**Author:** [@celstark](https://discourse.slicer.org/u/celstark)\
**Replies:** 27\
**Last updated:** [December 13, 2019, 12:00pm UTC](https://discourse.slicer.org/t/groups-tutorial-sample-data-guidance/6375 "2019-12-13T12:00:35Z")

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I’m looking to take FreeSurfer segmentations of the hippocampus and identify any pre/post intervention changes in shape. I’ve gone through the very nice tutorial on getting SPHARM run on all my segmentations and I’ve go…

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## [Use coefficients to reconstruct ](https://discourse.slicer.org/t/use-coefficients-to-reconstruct/8870)

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**Author:** [@Yoda0612](https://discourse.slicer.org/u/Yoda0612)\
**Replies:** 4\
**Last updated:** [October 28, 2019, 4:54am UTC](https://discourse.slicer.org/t/use-coefficients-to-reconstruct/8870 "2019-10-28T04:54:39Z")

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I applied SHPARM-PDM extension, and then obtained the coefficients of spherical harmonic. I wonder if I can reconstruct the original mode by just use the coefficients.

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## [ParaToSPHARMMesh completed with errors on win10](https://discourse.slicer.org/t/paratospharmmesh-completed-with-errors-on-win10/4814)

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**Author:** [@lxgwd1983](https://discourse.slicer.org/u/lxgwd1983)\
**Replies:** 18\
**Last updated:** [October 4, 2019, 4:42pm UTC](https://discourse.slicer.org/t/paratospharmmesh-completed-with-errors-on-win10/4814 "2019-10-04T16:42:14Z")

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Operating system:win 10 version:SlicerSALT 1.1.0-2018-10-25 I use the example data download from the web. The output of step1 and step2 are correct. but I meet an error on step3. there isn’t any more debug informati…

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## [SlicerSALT 2.2.1 Release: Summary and Changelog](https://discourse.slicer.org/t/slicersalt-2-2-1-release-summary-and-changelog/8450)

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**Author:** [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Replies:** 0\
**Last updated:** [September 16, 2019, 6:32pm UTC](https://discourse.slicer.org/t/slicersalt-2-2-1-release-summary-and-changelog/8450 "2019-09-16T18:32:59Z")

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The SlicerSALT team is proud to announce that version 2.2.1 is now available for download. This release introduces new features in almost all of our modules as well as dozens of bug fixes for better performance and stabi…

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## [Errors with GenParaMesh](https://discourse.slicer.org/t/errors-with-genparamesh/8377)

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**Author:** [@ytaneja](https://discourse.slicer.org/u/ytaneja)\
**Replies:** 5\
**Last updated:** [September 12, 2019, 5:58pm UTC](https://discourse.slicer.org/t/errors-with-genparamesh/8377 "2019-09-12T17:58:46Z")

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Hello, Whenever I run the GenParaMesh step with my segmentation (which has successfully gone through the SegPostProcess step), it results in this error through Slicer 4.8.1, Slicer 4.10.2, and Slicer SALT 2.0.0. I reali…

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## [SPHARM-PDM from triangular meshes](https://discourse.slicer.org/t/spharm-pdm-from-triangular-meshes/6938)

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**Author:** [@Fiona\_Pye](https://discourse.slicer.org/u/Fiona_Pye)\
**Replies:** 23\
**Last updated:** [August 19, 2019, 11:09am UTC](https://discourse.slicer.org/t/spharm-pdm-from-triangular-meshes/6938 "2019-08-19T11:09:43Z")

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I would like to apply the SPHARM-PDM to triangular meshes for palaeontological morphometrics. I first saw this method applied in SPHARM-MAT of Styner (2006) http://www.iu.edu/~spharm/SPHARM-docs/C03\_Spherical\_Parameteri…

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## [Error while building SlicerSALT](https://discourse.slicer.org/t/error-while-building-slicersalt/7926)

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**Author:** [@lbumbolo](https://discourse.slicer.org/u/lbumbolo)\
**Replies:** 1\
**Last updated:** [August 15, 2019, 6:16pm UTC](https://discourse.slicer.org/t/error-while-building-slicersalt/7926 "2019-08-15T18:16:17Z")

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Hi, I try to build SlicerSALT by myself but after the make -j 6 I receive this error: CMake Error at CMake/ctkMacroGenerateMocs.cmake:30 (QT5\_CREATE\_MOC\_COMMAND): QT5\_CREATE\_MOC\_COMMAND Function invoked with inco…

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## [MacOS Python Problem](https://discourse.slicer.org/t/macos-python-problem/7198)

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**Author:** [@iPsych](https://discourse.slicer.org/u/iPsych)\
**Replies:** 4\
**Last updated:** [June 27, 2019, 5:46am UTC](https://discourse.slicer.org/t/macos-python-problem/7198 "2019-06-27T05:46:56Z")

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The nightly version (1.1) 2019-06-14 doesn’t work in Mac. It can display .vtk files when imported, but Can’t process ANY SPHARM process. I also tested stable (1.0) version, but same issue. It’s weird since SlicerSa…

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## [Problems about ShapeAnalysisMANCOVA output——FDRP VS FDRP\_original](https://discourse.slicer.org/t/problems-about-shapeanalysismancova-output-fdrp-vs-fdrp-original/5083)

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**Author:** [@HanZhuang](https://discourse.slicer.org/u/HanZhuang)\
**Replies:** 3\
**Last updated:** [December 17, 2018, 11:14am UTC](https://discourse.slicer.org/t/problems-about-shapeanalysismancova-output-fdrp-vs-fdrp-original/5083 "2018-12-17T11:14:03Z")

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Operating system:Linux 14.04 LTS Slicer version:Slicer-4.8.1-linux-amd64, spharm-pdm\_v1.12\_linux64 While doing ShapeAnalysisMANCOVA, I encountered some problems. I used the ShapePopulationViewer to view the results. I …

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## [Some problems with 3Dslicer shape analysis-MANCOVA](https://discourse.slicer.org/t/some-problems-with-3dslicer-shape-analysis-mancova/4650)

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**Author:** [@HanZhuang](https://discourse.slicer.org/u/HanZhuang)\
**Replies:** 2\
**Last updated:** [November 8, 2018, 7:06am UTC](https://discourse.slicer.org/t/some-problems-with-3dslicer-shape-analysis-mancova/4650 "2018-11-08T07:06:09Z")

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Operating system:Linux 14.04 LTS Slicer version:Slicer-4.8.1-linux-amd64 Expected behavior: Recently, I am using 3D Slicer to do morphological analysis of brain structure.What I expected was that all the images put in…

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## [Inward\_outward dicplacement](https://discourse.slicer.org/t/inward-outward-dicplacement/3034)

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**Author:** [@Olof](https://discourse.slicer.org/u/Olof)\
**Replies:** 3\
**Last updated:** [July 11, 2018, 12:02pm UTC](https://discourse.slicer.org/t/inward-outward-dicplacement/3034 "2018-07-11T12:02:53Z")

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Dear Martin and Beatriz, running spharm I am a bit confused by my results. On the left side it seems to be a displacement towards the medial part of the brain … causing an deflation of the medial anterior and medial …

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## [Procrustes alignment ](https://discourse.slicer.org/t/procrustes-alignment/3144)

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**Author:** [@Pugliese](https://discourse.slicer.org/u/Pugliese)\
**Replies:** 2\
**Last updated:** [July 8, 2018, 3:02am UTC](https://discourse.slicer.org/t/procrustes-alignment/3144 "2018-07-08T03:02:58Z")

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Hi, Beatriz and Martin I was following the tutorial, and I noticed that the rigid-body Procrustes alignment (only translation and/or a rotation) can be used. I was just wondering how the size would be removed (rescalin…

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## [How to perform group analysis after getting the data form SPHARM-PDM 3D-slicer4.8 in MAC\_OS](https://discourse.slicer.org/t/how-to-perform-group-analysis-after-getting-the-data-form-spharm-pdm-3d-slicer4-8-in-mac-os/3314)

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**Author:** [@Kailiang\_Wang](https://discourse.slicer.org/u/Kailiang_Wang)\
**Replies:** 0\
**Last updated:** [June 27, 2018, 1:00pm UTC](https://discourse.slicer.org/t/how-to-perform-group-analysis-after-getting-the-data-form-spharm-pdm-3d-slicer4-8-in-mac-os/3314 "2018-06-27T13:00:29Z")

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Dear experts: I have performed the analysis of SPHARM-PDM 3D-slicer4.8 using the ShapeAnalysis\_Data\_Example in MCA\_OS. But I can’t find any valid tool to go on comparing these two groups in slicer of MAC\_OS, and I don’t…

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## [Interpreting the movement right?](https://discourse.slicer.org/t/interpreting-the-movement-right/2956)

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**Author:** [@Olof](https://discourse.slicer.org/u/Olof)\
**Replies:** 3\
**Last updated:** [June 4, 2018, 12:31pm UTC](https://discourse.slicer.org/t/interpreting-the-movement-right/2956 "2018-06-04T12:31:35Z")

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Dear Martin and Beatriz, trying to understand the movement of the hippocampus in this clinical group (compared to control) thus statistical map and diff mesh vector above. My interpretation is that apart from atroph…

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## [Small differences](https://discourse.slicer.org/t/small-differences/2825)

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**Author:** [@Olof](https://discourse.slicer.org/u/Olof)\
**Replies:** 1\
**Last updated:** [May 24, 2018, 7:39pm UTC](https://discourse.slicer.org/t/small-differences/2825 "2018-05-24T19:39:57Z")

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Hi Martin and Beau, I am running a shape analysis in which there are very small differences between groups - and at some points one group is larger than the other - in other places it is the opposite … Using the old …

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## [Missing option “Use mean as template”](https://discourse.slicer.org/t/missing-option-use-mean-as-template/2198)

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**Author:** [@kullboys](https://discourse.slicer.org/u/kullboys)\
**Replies:** 1\
**Last updated:** [May 9, 2018, 4:27am UTC](https://discourse.slicer.org/t/missing-option-use-mean-as-template/2198 "2018-05-09T04:27:33Z")

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Hello everyone working furhter with Spharm in Slicer-salt I realise there is two thing that was available before that I cannot find now. Use mean as template, The possibility to cancel a run when it is started. The on…

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