# SlicerSALT

**URL:** https://discourse.slicer.org/c/community/slicer-salt/14.md?page=1

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

**Page:** 2

---

## [A problem with USING SPHARM-PDM generator](https://discourse.slicer.org/t/a-problem-with-using-spharm-pdm-generator/25668)

<div class="topic-metadata">

**Author:** [@wael\_telha](https://discourse.slicer.org/u/wael_telha)\
**Replies:** 3\
**Last updated:** [November 14, 2022, 2:51pm UTC](https://discourse.slicer.org/t/a-problem-with-using-spharm-pdm-generator/25668 "2022-11-14T14:51:39Z")

</div>

the steps is the out of the DICOM i made a model that was saved as STL for the mandible as follow then i clipped a condyle and saved as a vtk for further work on SPHARM PDM-generator when i took this saved VTK to…

---

## [Signed distance from mean shape and output csv/txt file for 400 subjects](https://discourse.slicer.org/t/signed-distance-from-mean-shape-and-output-csv-txt-file-for-400-subjects/23490)

<div class="topic-metadata">

**Author:** [@Khalid\_Saifullah](https://discourse.slicer.org/u/Khalid_Saifullah)\
**Replies:** 10\
**Last updated:** [September 12, 2022, 11:45pm UTC](https://discourse.slicer.org/t/signed-distance-from-mean-shape-and-output-csv-txt-file-for-400-subjects/23490 "2022-09-12T23:45:50Z")

</div>

Hi all! I am using SPHARM-PDM to generate shapes of subcortical structures. Using the output files “SubjectName\_pp\_surf\_SPHARM\_procalign.vtk”, I produced a mean vtk file with “Shape Variation Analyzer” module. My next …

---

## [SPHARM flip option](https://discourse.slicer.org/t/spharm-flip-option/16681)

<div class="topic-metadata">

**Author:** [@ikhsannk](https://discourse.slicer.org/u/ikhsannk)\
**Replies:** 2\
**Last updated:** [August 22, 2022, 4:05pm UTC](https://discourse.slicer.org/t/spharm-flip-option/16681 "2022-08-22T16:05:37Z")

</div>

Hello Bea @bpaniagua , Martin @styner and everyone. I have a simple question regarding SPHARM, is there a way to manually flip the output SPHARM file within SlicerSALT? I am aware that there are ‘flip template’ and ‘…

---

## [Model to Model Distance Parameters](https://discourse.slicer.org/t/model-to-model-distance-parameters/6543)

<div class="topic-metadata">

**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 11\
**Last updated:** [August 19, 2022, 12:47pm UTC](https://discourse.slicer.org/t/model-to-model-distance-parameters/6543 "2022-08-19T12:47:42Z")

</div>

What are the differences between the parameters in model to model distance? By that I mean, what’s the differences between absolute closest point, signed closest point, and closest point? How do these differences effect …

---

## [Group analysis with SPHARM-PDM](https://discourse.slicer.org/t/group-analysis-with-spharm-pdm/885)

<div class="topic-metadata">

**Author:** [@laurapascal](https://discourse.slicer.org/u/laurapascal)\
**Replies:** 11\
**Last updated:** [August 8, 2022, 8:47am UTC](https://discourse.slicer.org/t/group-analysis-with-spharm-pdm/885 "2022-08-08T08:47:25Z")

</div>

Interesting questions form Panos about group analysis with SPHARM-PDM tool: I am trying to compare regional differences in hippocampal structure between three groups (2 diseased groups, and one healthy control group), …

---

## [ParatoSPHARMMesh Error](https://discourse.slicer.org/t/paratospharmmesh-error/24176)

<div class="topic-metadata">

**Author:** [@Hoai-Nam\_Bui](https://discourse.slicer.org/u/Hoai-Nam_Bui)\
**Replies:** 0\
**Last updated:** [July 4, 2022, 10:31pm UTC](https://discourse.slicer.org/t/paratospharmmesh-error/24176 "2022-07-04T22:31:20Z")

</div>

Hello! I am running into a FORTRAN error during Step 3 of SPHARM Generator on SlicerSalt 3.0 win10. When using a different dataset (caiman vertebrae) I don’t run into this error, however it seems to be the case with th…

---

## [Some problems about SegPostProcess](https://discourse.slicer.org/t/some-problems-about-segpostprocess/23845)

<div class="topic-metadata">

**Author:** [@yuanzhen\_cui](https://discourse.slicer.org/u/yuanzhen_cui)\
**Replies:** 5\
**Last updated:** [June 14, 2022, 9:19am UTC](https://discourse.slicer.org/t/some-problems-about-segpostprocess/23845 "2022-06-14T09:19:10Z")

</div>

Operating system:MacOs Slicer version:4.1120210226 Expected behavior:I try to execute the SegPostProcess with the example names “InputImage.nrrd” which download from the slicerssalt workshop. Actual behavior:The Log m…

---

## [SPHARM-PDM Euler Number problem](https://discourse.slicer.org/t/spharm-pdm-euler-number-problem/2745)

<div class="topic-metadata">

**Author:** [@doganarda](https://discourse.slicer.org/u/doganarda)\
**Replies:** 9\
**Last updated:** [June 12, 2022, 2:54pm UTC](https://discourse.slicer.org/t/spharm-pdm-euler-number-problem/2745 "2022-06-12T14:54:44Z")

</div>

Hello everyone, For my M.Sc. Thesis work, I need to apply SPHARM-PDM analysis to certain number of segmented hippocampi from an experiment but I am really new to the program and I still cannot make sense out of it clear…

---

## [SPHARM-PDM: Different morphology from a model maker and SPHARM](https://discourse.slicer.org/t/spharm-pdm-different-morphology-from-a-model-maker-and-spharm/22711)

<div class="topic-metadata">

**Author:** [@Bryan\_Jung](https://discourse.slicer.org/u/Bryan_Jung)\
**Replies:** 2\
**Last updated:** [March 28, 2022, 5:01pm UTC](https://discourse.slicer.org/t/spharm-pdm-different-morphology-from-a-model-maker-and-spharm/22711 "2022-03-28T17:01:38Z")

</div>

Dear Slicer community, I am teaching myself how to use SPHARM-PDM for my future research projects. I have been using publicly available CBCT images. Recently, I successfully segmented a TMJ from a CBCT file using ITK-Sn…

---

## [Close slicersalt after processing in commandline](https://discourse.slicer.org/t/close-slicersalt-after-processing-in-commandline/21159)

<div class="topic-metadata">

**Author:** [@iPsych](https://discourse.slicer.org/u/iPsych)\
**Replies:** 1\
**Last updated:** [December 22, 2021, 3:52am UTC](https://discourse.slicer.org/t/close-slicersalt-after-processing-in-commandline/21159 "2021-12-22T03:52:56Z")

</div>

Running slicersalt via commandline seems very useful, but seems not-loop friendly. Is it possible to stop slicersalt, after ./slicersalt --no-main-window --python-script SOME COMMAND? after successful run, the cmd sto…

---

## [Calculating the axes of the ellipsoid part of the shape from l=1 coefficients](https://discourse.slicer.org/t/calculating-the-axes-of-the-ellipsoid-part-of-the-shape-from-l-1-coefficients/20920)

<div class="topic-metadata">

**Author:** [@hcc](https://discourse.slicer.org/u/hcc)\
**Replies:** 2\
**Last updated:** [December 7, 2021, 11:54am UTC](https://discourse.slicer.org/t/calculating-the-axes-of-the-ellipsoid-part-of-the-shape-from-l-1-coefficients/20920 "2021-12-07T11:54:43Z")

</div>

Hi there, really enjoying using the great tools of SPHARM-PDM. I just wanted to know how I could go about finding the 3 axes of the ellipsoid part of my shape in object space (not for alignment purposes, rather for some…

---

## [Correspondent Point Calculations](https://discourse.slicer.org/t/correspondent-point-calculations/19872)

<div class="topic-metadata">

**Author:** [@Daniel1](https://discourse.slicer.org/u/Daniel1)\
**Replies:** 0\
**Last updated:** [September 26, 2021, 4:32pm UTC](https://discourse.slicer.org/t/correspondent-point-calculations/19872 "2021-09-26T16:32:57Z")

</div>

Hey guys, I’ve got two models. They have been registered on 3D Slicer with CMFReg. A SPHARM mesh has been generated for each using SlicerSalt. So far so good. How do I go about automatically identifying corresponding…

---

## [Is there any way to get SPHARM-PDM output when running from cmd?](https://discourse.slicer.org/t/is-there-any-way-to-get-spharm-pdm-output-when-running-from-cmd/19853)

<div class="topic-metadata">

**Author:** [@Robert\_Michael\_Sharp](https://discourse.slicer.org/u/Robert_Michael_Sharp)\
**Replies:** 1\
**Last updated:** [September 25, 2021, 5:01pm UTC](https://discourse.slicer.org/t/is-there-any-way-to-get-spharm-pdm-output-when-running-from-cmd/19853 "2021-09-25T17:01:27Z")

</div>

I’m having a problem where I have created a mac application that calls SPHARM-PDM and informs the user as files are created by reading the terminal output and searching for “CASE completed”, however, when trying to port …

---

## [Some questions about SPHARM-PDM, alignment, and registration](https://discourse.slicer.org/t/some-questions-about-spharm-pdm-alignment-and-registration/10499)

<div class="topic-metadata">

**Author:** [@keven](https://discourse.slicer.org/u/keven)\
**Replies:** 5\
**Last updated:** [July 29, 2021, 8:21am UTC](https://discourse.slicer.org/t/some-questions-about-spharm-pdm-alignment-and-registration/10499 "2021-07-29T08:21:57Z")

</div>

Dear experts : Recently，I read a paper, Clinical application of SPHARM-PDM to quantify temporomandibular joint osteoarthritis, which was published in the Computerized Medical Imaging and Graphics in 2011. This is a bri…

---

## [Shape Population Viewer](https://discourse.slicer.org/t/shape-population-viewer/13593)

<div class="topic-metadata">

**Author:** [@Madelene\_Habib](https://discourse.slicer.org/u/Madelene_Habib)\
**Replies:** 3\
**Last updated:** [July 9, 2021, 5:22am UTC](https://discourse.slicer.org/t/shape-population-viewer/13593 "2021-07-09T05:22:12Z")

</div>

Operating system: Windows 10 Slicer version: 4.10.2 I’m trying to use the ‘shape population view’ module, when I installed and restarted 3Dslicer it does not show up when i search for the module. I tried reinstalling 3…

---

## [Feature discussion: Deep learning module in SlicerSALT](https://discourse.slicer.org/t/feature-discussion-deep-learning-module-in-slicersalt/7731)

<div class="topic-metadata">

**Author:** [@styner](https://discourse.slicer.org/u/styner)\
**Replies:** 3\
**Last updated:** [July 8, 2021, 3:25pm UTC](https://discourse.slicer.org/t/feature-discussion-deep-learning-module-in-slicersalt/7731 "2021-07-08T15:25:56Z")

</div>

This is a discussion page for a new feature in SlicerSALT under development. Goal: Add a module to SlicerSALT allowing for deep learning classification support. Features: python module use of keras for deep learning n…

---

## [SPHARM-PDM surface point parameter extraction](https://discourse.slicer.org/t/spharm-pdm-surface-point-parameter-extraction/18472)

<div class="topic-metadata">

**Author:** [@Ian\_Harding](https://discourse.slicer.org/u/Ian_Harding)\
**Replies:** 0\
**Last updated:** [July 2, 2021, 3:18am UTC](https://discourse.slicer.org/t/spharm-pdm-surface-point-parameter-extraction/18472 "2021-07-02T03:18:56Z")

</div>

After running group-level statistical models on the SPHARM surfaces, and generating 3D illustrations of areas that are significantly related to our independent variable of interest, I am curious whether it is possible to…

---

## [CT brain import data](https://discourse.slicer.org/t/ct-brain-import-data/17533)

<div class="topic-metadata">

**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 3\
**Last updated:** [May 10, 2021, 8:54pm UTC](https://discourse.slicer.org/t/ct-brain-import-data/17533 "2021-05-10T20:54:02Z")

</div>

I tried to load a 1mm brain CT image, but the software hungs. The CT mage is in nrrd file format.

---

## [Correlation analysis of shape parameters with a continuous variable](https://discourse.slicer.org/t/correlation-analysis-of-shape-parameters-with-a-continuous-variable/16252)

<div class="topic-metadata">

**Author:** [@Adarsh\_Ghosh](https://discourse.slicer.org/u/Adarsh_Ghosh)\
**Replies:** 0\
**Last updated:** [February 27, 2021, 4:12am UTC](https://discourse.slicer.org/t/correlation-analysis-of-shape-parameters-with-a-continuous-variable/16252 "2021-02-27T04:12:41Z")

</div>

Hello! I am new to shape analysis in general and I want to correlate a continuous pathological variable ( for example % of necrosis) with shape of a lesion ( I assume spherical topology). I assume Covariate Significanc…

---

## [Covariate Significance Testing - multiple covariate testing problem(s)](https://discourse.slicer.org/t/covariate-significance-testing-multiple-covariate-testing-problem-s/16036)

<div class="topic-metadata">

**Author:** [@ikhsannk](https://discourse.slicer.org/u/ikhsannk)\
**Replies:** 0\
**Last updated:** [February 17, 2021, 5:29pm UTC](https://discourse.slicer.org/t/covariate-significance-testing-multiple-covariate-testing-problem-s/16036 "2021-02-17T17:29:48Z")

</div>

Hello, my name is Ikhsan and I have some questions regarding multiple covariate testing on the Covariate Significance Testing module. Before that, I have followed the tutorial using the example dataset (bump\*\*.vtk) prov…

---

## [SPHARM-PDM alignment ](https://discourse.slicer.org/t/spharm-pdm-alignment/15943)

<div class="topic-metadata">

**Author:** [@ikhsannk](https://discourse.slicer.org/u/ikhsannk)\
**Replies:** 4\
**Last updated:** [February 16, 2021, 3:45pm UTC](https://discourse.slicer.org/t/spharm-pdm-alignment/15943 "2021-02-16T15:45:56Z")

</div>

Hello, Beatriz, Martin, and others. My name is Ikhsan and I would like to ask a few things regarding SPHARM-PDM. Firstly, I have looked at the tutorial and worked on the hippocampus example dataset. It functions properl…

---

## [Problems with the SPHARM-PDM on Slicer-4.8.0-linux-amd64 (Command-Line Tool, the step GenParaMesh)](https://discourse.slicer.org/t/problems-with-the-spharm-pdm-on-slicer-4-8-0-linux-amd64-command-line-tool-the-step-genparamesh/15877)

<div class="topic-metadata">

**Author:** [@Daisy\_Xiong](https://discourse.slicer.org/u/Daisy_Xiong)\
**Replies:** 0\
**Last updated:** [February 7, 2021, 4:31am UTC](https://discourse.slicer.org/t/problems-with-the-spharm-pdm-on-slicer-4-8-0-linux-amd64-command-line-tool-the-step-genparamesh/15877 "2021-02-07T04:31:43Z")

</div>

Hello, everyone, I tried to utilize the software Slicer(Slicer-4.8.0-linux-amd64) and the method SPHARM-PDM to get the some SPHARM Mesh ( such as the output files \*para.vtk and \*SPHARM\_Ellalign.vtk). If I use the main …

---

## [Failed to establish point to point coreposndence](https://discourse.slicer.org/t/failed-to-establish-point-to-point-coreposndence/15735)

<div class="topic-metadata">

**Author:** [@Maxibers](https://discourse.slicer.org/u/Maxibers)\
**Replies:** 2\
**Last updated:** [February 1, 2021, 9:20pm UTC](https://discourse.slicer.org/t/failed-to-establish-point-to-point-coreposndence/15735 "2021-02-01T21:20:27Z")

</div>

I’m having trouble in establishing point to point corespondence. Long story short i’m trying to analyze tmj condyle heads remodeling. So after the SPHARM-PDM process on some, but not all, the condyle heads i cannot get …

---

## [Group comparison with shape regression ](https://discourse.slicer.org/t/group-comparison-with-shape-regression/14561)

<div class="topic-metadata">

**Author:** [@orangekic](https://discourse.slicer.org/u/orangekic)\
**Replies:** 0\
**Last updated:** [November 12, 2020, 12:35pm UTC](https://discourse.slicer.org/t/group-comparison-with-shape-regression/14561 "2020-11-12T12:35:59Z")

</div>

I want to perform a statistical group comparison with shape regression. Is there any tutorial regarding this analysis? Which module should I use (“GROUP” or “Shape Regression”)? Thank you very much.

---

## [FDR or Multiple Comparison Corection in Covariate Significance Testing](https://discourse.slicer.org/t/fdr-or-multiple-comparison-corection-in-covariate-significance-testing/13953)

<div class="topic-metadata">

**Author:** [@iPsych](https://discourse.slicer.org/u/iPsych)\
**Replies:** 1\
**Last updated:** [October 13, 2020, 1:40pm UTC](https://discourse.slicer.org/t/fdr-or-multiple-comparison-corection-in-covariate-significance-testing/13953 "2020-10-13T13:40:41Z")

</div>

Hi, Does the Covariate Significance Testing include any FDR or Multiple Comparison Correction method in its pipeline? I read carefully the documentation, but found no information about it. If not, is there any recommen…

---

## [FreeSurfer data import not showing segments](https://discourse.slicer.org/t/freesurfer-data-import-not-showing-segments/13258)

<div class="topic-metadata">

**Author:** [@averyw](https://discourse.slicer.org/u/averyw)\
**Replies:** 0\
**Last updated:** [August 31, 2020, 4:21pm UTC](https://discourse.slicer.org/t/freesurfer-data-import-not-showing-segments/13258 "2020-08-31T16:21:20Z")

</div>

I am running SlicerSALT 3.0 on my Macbook and using the FreeSurfer data import. When I choose the directories in Data Importer, all subjects show up but nothing shows up in the segments table. I downloaded SlicerSALT 2.1…

---

## [SlicerSalt Data CSV Import Not Working](https://discourse.slicer.org/t/slicersalt-data-csv-import-not-working/13252)

<div class="topic-metadata">

**Author:** [@Violet\_Evans](https://discourse.slicer.org/u/Violet_Evans)\
**Replies:** 3\
**Last updated:** [August 31, 2020, 3:49pm UTC](https://discourse.slicer.org/t/slicersalt-data-csv-import-not-working/13252 "2020-08-31T15:49:38Z")

</div>

My Mac SlicerSalt CSV Import button is not letting me type into the text box and no dialogue box appears when the CSV button is clicked.

---

## [Consistent ordering of surface points on meshes generated by SPHARM-PDM](https://discourse.slicer.org/t/consistent-ordering-of-surface-points-on-meshes-generated-by-spharm-pdm/12955)

<div class="topic-metadata">

**Author:** [@Zhiy](https://discourse.slicer.org/u/Zhiy)\
**Replies:** 2\
**Last updated:** [August 16, 2020, 7:56pm UTC](https://discourse.slicer.org/t/consistent-ordering-of-surface-points-on-meshes-generated-by-spharm-pdm/12955 "2020-08-16T19:56:09Z")

</div>

Hi, I am using SPHARM-PDM downloaded from spharm-pdm\_v1.13\_linux64.zip. My inputs are binary image files (\*.nrrd). My expectation is that SPHARM-PDM can output triangle meshes that have a consistent ordering on the sur…

---

## [Partial correlation](https://discourse.slicer.org/t/partial-correlation/12394)

<div class="topic-metadata">

**Author:** [@quentin\_devignes](https://discourse.slicer.org/u/quentin_devignes)\
**Replies:** 4\
**Last updated:** [July 29, 2020, 3:17pm UTC](https://discourse.slicer.org/t/partial-correlation/12394 "2020-07-29T15:17:33Z")

</div>

Hello SlicerSALT Team, As far as partial correlation can not be done with shapeAnalysisMANCOVA, do you know I could perform it? I thought I could use the distance at each vertex between my patients’ shapes and the mean …

---

## [Could use a model like \*.vtk or \*.obj as the input of SPHARM?](https://discourse.slicer.org/t/could-use-a-model-like-vtk-or-obj-as-the-input-of-spharm/12599)

<div class="topic-metadata">

**Author:** [@Yoda0612](https://discourse.slicer.org/u/Yoda0612)\
**Replies:** 3\
**Last updated:** [July 27, 2020, 9:15pm UTC](https://discourse.slicer.org/t/could-use-a-model-like-vtk-or-obj-as-the-input-of-spharm/12599 "2020-07-27T21:15:51Z")

</div>

I would like to obtain the spherical harmonic coefficients for a model. However, SPHARM ask me to input the binary image or vtk model with para model. I just have a model without para model. How could I obtain spheric…

[Previous page](https://discourse.slicer.org/c/community/slicer-salt/14.md)

[Next page](https://discourse.slicer.org/c/community/slicer-salt/14.md?page=2)