# \#spharm-pdm **URL:** https://discourse.slicer.org/tag/spharm-pdm/62.md [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) --- ## [Acquisition of coordinates post SPHARM/Procrustes for analysis](https://discourse.slicer.org/t/acquisition-of-coordinates-post-spharm-procrustes-for-analysis/32643)
**Author:** [@Hoai-Nam\_Bui](https://discourse.slicer.org/u/Hoai-Nam_Bui)\ **Replies:** 0\ **Last updated:** [November 7, 2023, 3:41pm UTC](https://discourse.slicer.org/t/acquisition-of-coordinates-post-spharm-procrustes-for-analysis/32643 "2023-11-07T15:41:05Z")
Good morning! I have a dataset of 51 different vertebrae I am analyzing for shape variation. I’ve utilized the population analysis module to export the PCA data in the json format and acquired the first two PCs from the… --- ## [SPHARM-PDM correspondence imrpovement](https://discourse.slicer.org/t/spharm-pdm-correspondence-imrpovement/35503)
**Author:** [@samia](https://discourse.slicer.org/u/samia)\ **Replies:** 0\ **Last updated:** [April 15, 2024, 5:00pm UTC](https://discourse.slicer.org/t/spharm-pdm-correspondence-imrpovement/35503 "2024-04-15T17:00:11Z")
Hello , i have a question about the correspondence improvement in SPHARM- PDM module after adding the landmarks i got two folders that contains the aligned models and the rotated sphere is it possible or how can i check … --- ## [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)
**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")
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… --- ## [SPHARM-PDM runtime](https://discourse.slicer.org/t/spharm-pdm-runtime/34666)
**Author:** [@samia](https://discourse.slicer.org/u/samia)\ **Replies:** 0\ **Last updated:** [March 3, 2024, 3:16am UTC](https://discourse.slicer.org/t/spharm-pdm-runtime/34666 "2024-03-03T03:16:45Z")
Hello , i’m using SPHARM-PDM module in slicerSalt to represent the tooth using spherical harmonics but the run time for the parametrization part is taking to much time (one hour and sometimes more ) for only one tooth. I… --- ## [SPHARM-PDM Error: 'SegPostProcess terminated with a numerical fault'](https://discourse.slicer.org/t/spharm-pdm-error-segpostprocess-terminated-with-a-numerical-fault/34519)
**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")
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… --- ## [Seeking Guidance on Ventricle Shape Analysis in 3D Slicer](https://discourse.slicer.org/t/seeking-guidance-on-ventricle-shape-analysis-in-3d-slicer/32364)
**Author:** [@Julius\_Bogomolovas](https://discourse.slicer.org/u/Julius_Bogomolovas)\ **Replies:** 4\ **Last updated:** [October 26, 2023, 8:47pm UTC](https://discourse.slicer.org/t/seeking-guidance-on-ventricle-shape-analysis-in-3d-slicer/32364 "2023-10-26T20:47:16Z")
Hello 3D Slicer community, First and foremost, I’d like to express my gratitude for your dedication to developing and maintaining this powerful set of tools for shape analysis. So this is gonna be a multifaceted post, b… --- ## [Aligned SPHARM models flip inside out during PCA](https://discourse.slicer.org/t/aligned-spharm-models-flip-inside-out-during-pca/30768)
**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")
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 … --- ## [Normalisation or scaling with SPHARM](https://discourse.slicer.org/t/normalisation-or-scaling-with-spharm/23602)
**Author:** [@Khalid\_Saifullah](https://discourse.slicer.org/u/Khalid_Saifullah)\ **Replies:** 9\ **Last updated:** [August 30, 2022, 7:05am UTC](https://discourse.slicer.org/t/normalisation-or-scaling-with-spharm/23602 "2022-08-30T07:05:26Z")
Hi, I would like to normalise all of my SPHARM-PDM output subjects (subjectID\_pp\_surf\_SPHARM\_procalign.vtk) by a scale factor before running any sort of statistical analysis. I am going to use a separate tool for the st… --- ## [Group analysis with SPHARM-PDM](https://discourse.slicer.org/t/group-analysis-with-spharm-pdm/885)
**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")
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), … --- ## [Commandline SPHARM-PDM using parameter options](https://discourse.slicer.org/t/commandline-spharm-pdm-using-parameter-options/24609)
**Author:** [@Khalid\_Saifullah](https://discourse.slicer.org/u/Khalid_Saifullah)\ **Replies:** 0\ **Last updated:** [August 2, 2022, 10:11pm UTC](https://discourse.slicer.org/t/commandline-spharm-pdm-using-parameter-options/24609 "2022-08-02T22:11:03Z")
Hi! I am trying to run the 3 steps of SPHARM-PDM separately using commandline options. I can see that SlicerSALT has a commandline option but this generates all the 3 steps together i.e. just like how you could run them… --- ## [ParatoSPHARMMesh Error](https://discourse.slicer.org/t/paratospharmmesh-error/24176)
**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")
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… --- ## [Mandible spharm pdm](https://discourse.slicer.org/t/mandible-spharm-pdm/22273)
**Author:** [@lili-yu22](https://discourse.slicer.org/u/lili-yu22)\ **Replies:** 0\ **Last updated:** [March 3, 2022, 2:28am UTC](https://discourse.slicer.org/t/mandible-spharm-pdm/22273 "2022-03-03T02:28:24Z")
Dear expert first，l segment the mandible，then split it into two half. 2.l choose the right part，then copy it .l cut the copy short. 3.then both part use spharm-pdm. 4. in the modeltomodeldistance the right mandible… --- ## [Shape analysis using MFSDA](https://discourse.slicer.org/t/shape-analysis-using-mfsda/18018)
**Author:** [@iyerkrithika21](https://discourse.slicer.org/u/iyerkrithika21)\ **Replies:** 6\ **Last updated:** [September 7, 2021, 1:11pm UTC](https://discourse.slicer.org/t/shape-analysis-using-mfsda/18018 "2021-09-07T13:11:56Z")
Trying to run the Covariates Significance Test with SlicerSALT 3.0.0 The program fails if the selected folder to store the output values is empty If pvalues.json and output.vtk are some empty files placed in the output… --- ## [Some questions about SPHARM-PDM, alignment, and registration](https://discourse.slicer.org/t/some-questions-about-spharm-pdm-alignment-and-registration/10499)
**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")
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… --- ## [Meshes won't process in SPHARM-PDM Generator](https://discourse.slicer.org/t/meshes-wont-process-in-spharm-pdm-generator/18085)
**Author:** [@quan](https://discourse.slicer.org/u/quan)\ **Replies:** 0\ **Last updated:** [June 11, 2021, 9:47pm UTC](https://discourse.slicer.org/t/meshes-wont-process-in-spharm-pdm-generator/18085 "2021-06-11T21:47:12Z")
Hi!! I’m trying to run a few meshes through the SPHARM-PDM generator. My process is as follow: Import .stl files Convert .stl to binary label map .nrrd Input the .nrrd into the SPHARM-PDM generator pipeline Change some… --- ## [Failed to establish point to point coreposndence](https://discourse.slicer.org/t/failed-to-establish-point-to-point-coreposndence/15735)
**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")
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 … --- ## [Equation for medial axis from SPHARM-PDM](https://discourse.slicer.org/t/equation-for-medial-axis-from-spharm-pdm/12311)
**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")
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… --- ## [Question on .coef output file](https://discourse.slicer.org/t/question-on-coef-output-file/10979)
**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")
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… --- ## [SPHARM analysis of 3D slicer](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630)
**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")
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 … --- ## [SPHARM-PDM Shape Analysis Module Failing](https://discourse.slicer.org/t/spharm-pdm-shape-analysis-module-failing/8209)
**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\ **Replies:** 4\ **Last updated:** [September 11, 2019, 5:49am UTC](https://discourse.slicer.org/t/spharm-pdm-shape-analysis-module-failing/8209 "2019-09-11T05:49:14Z")
Hi, I am having some major issues getting SPHARM-PDM’s Shape Analysis Module to work. I have tried it on the newest nightly build from today, and a nightly build from 2018. When I input a folder containing mandible VTK f… --- ## [SPHARM-PDM not available in Slicer Extensions](https://discourse.slicer.org/t/spharm-pdm-not-available-in-slicer-extensions/6678)
**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\ **Replies:** 0\ **Last updated:** [May 2, 2019, 2:30pm UTC](https://discourse.slicer.org/t/spharm-pdm-not-available-in-slicer-extensions/6678 "2019-05-02T14:30:31Z")
Operating System: Windows 10 Slicer Distribution: 4.11.0-2019-05-01 r28202 The slicer extension manager is not displaying the SPHARM-PDM extension anymore. In addition, the appsite http://slicer.kitware.com/midas3/slic… --- ## [Batch processing with SPHARM-PDM](https://discourse.slicer.org/t/batch-processing-with-spharm-pdm/2119)
**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\ **Replies:** 4\ **Last updated:** [February 28, 2018, 4:28pm UTC](https://discourse.slicer.org/t/batch-processing-with-spharm-pdm/2119 "2018-02-28T16:28:31Z")
Hi, I am very new to coding in Python, so hopefully there might be an easy, straightforward tutorial, or possibly a way to circumvent the use of python coding altogether, but is there anything like this on how to perform… --- ## [SPHARM-PDM installation on Windows 10](https://discourse.slicer.org/t/spharm-pdm-installation-on-windows-10/979)
**Author:** [@laurapascal](https://discourse.slicer.org/u/laurapascal)\ **Replies:** 2\ **Last updated:** [September 25, 2017, 1:57pm UTC](https://discourse.slicer.org/t/spharm-pdm-installation-on-windows-10/979 "2017-09-25T13:57:50Z")
Catharina De Rosa wrote on Wed, August 30, 2017: I download extension to use Spharm-pdm on 3D Slicer for Windows 10. As I tried to use the tools, it also pop up mensages that the program has stopped working. Messages…