# SPHARM analysis of 3D slicer

**URL:** <https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630>\
**Category:** SlicerSALT\
**Tags:** spharm-pdm\
**Created:** [December 27, 2019, 7:24pm UTC](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630 "2019-12-27T19:24:54Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![keven](https://avatars.discourse-cdn.com/v4/letter/k/cdc98d/32.png) [@keven](https://discourse.slicer.org/u/keven)\
**Post date:** [December 27, 2019, 7:24pm UTC](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630/1 "2019-12-27T19:24:54Z")

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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 CBCT images of condyle in different periods, and then used itk-snap to complete the modeling and export them to VTK format, but when I imported folder, which contained the condyle VTK files, into the SPHARM module for shape analysis, the first and second steps can be completed, but the third step：ParaToSPHARMMesh completed with errors. The following shows the error points indicated by 3D Slicer, Can someone help me see where the problem is?  
Operating system:win 10  
version:3D Slicer 4.10.2

Thanks in advance!

 ![1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/2/327b54b004a9cc22c0c3751de5c765c42ed3fb31.png)

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**Author:** ![keven](https://avatars.discourse-cdn.com/v4/letter/k/cdc98d/32.png) [@keven](https://discourse.slicer.org/u/keven)\
**Post date:** [January 1, 2020, 3:30am UTC](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630/2 "2020-01-01T03:30:36Z")

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When I used SlicerSALT for SPHARM analysis of the same file, ONLY the third step completed with errors, as shown below. Does anyone know where the problem is?  
Case 0: 1111 - step 3: ParaToSPHARMMesh completed with errors  
loadNodeFromFile `returnNode` argument is deprecated. Loaded node is now returned directly if `returnNode` is not specified.

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**Author:** ![bpaniagua](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bpaniagua/32/20_2.png) [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Post date:** [January 2, 2020, 1:21pm UTC](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630/3 "2020-01-02T13:21:42Z")

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Hi Kaiwen,

Thank you for using SPHARM! Could you please try to repeat this process with the preview version of Slicer or using [our SlicerSALT package](https://data.kitware.com/#collection/586fbb7b8d777f05f44a5c7b/folder/5898b7ef8d777f07219fcb14)?

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**Author:** ![keven](https://avatars.discourse-cdn.com/v4/letter/k/cdc98d/32.png) [@keven](https://discourse.slicer.org/u/keven)\
**Post date:** [January 2, 2020, 2:11pm UTC](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630/4 "2020-01-02T14:11:23Z")

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Thank you very much for your reply!  
I tried to reanalyze the data using slicersalt 2.2.0.I changed the number of iterations to 100, and the other parameters remain default.  
The first and second steps can be completed, but the third step:ParaToSPHARMMesh completed with errors.  
Python Interactor showed me the following information:  
– Completing : Case 1: 2222 - step 2: GenParaMesh

– Completed : Case 1: 2222 - step 2: GenParaMesh

– Scheduled : Case 1: 2222 - step 3: ParaToSPHARMMesh

– Completed with errors : Case 1: 2222 - step 3: ParaToSPHARMMesh

Saving 2222.nrrd in D:/CT/2/Step0\_MeshToLabelMap

Saving 2222\_pp.nrrd in D:/CT/2/Step1\_SegPostProcess

Saving 2222\_pp\_para.vtk in D:/CT/2/Step2\_GenParaMesh

Saving 2222\_pp\_surf.vtk in D:/CT/2/Step2\_GenParaMesh

– Completed with errors: Case 1: 2222.vtk

Case 1 (2222.vtk) took 60 sec to run

Case 1: 2222 - step 3: ParaToSPHARMMesh completed with errors

All pipelines took: 182 sec to run

– Completed with errors : ShapeAnalysisModule

Case 1: 2222 - step 3: ParaToSPHARMMesh completed with errors

3.6.7 (default, Sep 6 2019, 16:48:27) [MSC v.1900 64 bit (AMD64)] on win32

> > >

Status: _Idle_

Widget: Running ShapeAnalysisModule

– Scheduled : ShapeAnalysisModule

2 case(s) found

– Running : ShapeAnalysisModule

loadNodeFromFile `returnNode` argument is deprecated. Loaded node is now returned directly if `returnNode` is not specified.

– Scheduled: Case 0: 1111.vtk

– Scheduled : Case 0: 1111 - step 0: Mesh To Label Map

– Running : Case 0: 1111 - step 0: Mesh To Label Map

– Completed : Case 0: 1111 - step 0: Mesh To Label Map

– Scheduled : Case 0: 1111 - step 1: SegPostProcess

– Running : Case 0: 1111 - step 1: SegPostProcess

– Completing : Case 0: 1111 - step 1: SegPostProcess

– Completed : Case 0: 1111 - step 1: SegPostProcess

– Scheduled : Case 0: 1111 - step 2: GenParaMesh

– Running : Case 0: 1111 - step 2: GenParaMesh

– Completing : Case 0: 1111 - step 2: GenParaMesh

– Completed : Case 0: 1111 - step 2: GenParaMesh

– Scheduled : Case 0: 1111 - step 3: ParaToSPHARMMesh

– Running : Case 0: 1111 - step 3: ParaToSPHARMMesh

– Completed with errors : Case 0: 1111 - step 3: ParaToSPHARMMesh

Saving 1111.nrrd in D:/CT/2/Step0\_MeshToLabelMap

Saving 1111\_pp.nrrd in D:/CT/2/Step1\_SegPostProcess

Saving 1111\_pp\_para.vtk in D:/CT/2/Step2\_GenParaMesh

Saving 1111\_pp\_surf.vtk in D:/CT/2/Step2\_GenParaMesh

– Completed with errors: Case 0: 1111.vtk

Case 0 (1111.vtk) took 121 sec to run

– Completed : Case 1: 2222 - step 0: Mesh To Label Map

– Scheduled : Case 1: 2222 - step 1: SegPostProcess

– Running : Case 1: 2222 - step 1: SegPostProcess

– Completed : Case 1: 2222 - step 1: SegPostProcess

– Scheduled : Case 1: 2222 - step 2: GenParaMesh

– Running : Case 1: 2222 - step 2: GenParaMesh

– Scheduled: Case 1: 2222.vtk

– Scheduled : Case 1: 2222 - step 0: Mesh To Label Map

– Running : Case 1: 2222 - step 0: Mesh To Label Map

Is this problem due to my mistake in operation or other reasons？  
I look forward to your reply！Thank you in advance！

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<div class="post-metadata">

**Author:** ![keven](https://avatars.discourse-cdn.com/v4/letter/k/cdc98d/32.png) [@keven](https://discourse.slicer.org/u/keven)\
**Post date:** [January 2, 2020, 2:14pm UTC](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630/5 "2020-01-02T14:14:47Z")

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What other information do I need to provide to help you analyze this problem?

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**Author:** ![bpaniagua](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bpaniagua/32/20_2.png) [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Post date:** [January 2, 2020, 2:35pm UTC](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630/6 "2020-01-02T14:35:26Z")

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What is the content of your paratospharm mesh folder?

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<div class="post-metadata">

**Author:** ![keven](https://avatars.discourse-cdn.com/v4/letter/k/cdc98d/32.png) [@keven](https://discourse.slicer.org/u/keven)\
**Post date:** [January 2, 2020, 3:00pm UTC](https://discourse.slicer.org/t/spharm-analysis-of-3d-slicer/9630/7 "2020-01-02T15:00:33Z")

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Hi ,Beatriz Paniagua!  
I followed your advice and used the 4.8.0 version of 3D slicer for SPHARM analysis.  
Surprisingly, when I import the VTK model file into 3D slicer, I can complete three steps of analysis. Here is a screenshot of the file contained in the third step folder, paratosparm.

 ![1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/f/4f23989e113b3363bc7be782cc205e991a46cf86.png)  
Does this mean that I have finished the SPHARM analysis？