NITRC SPHARM-PDM Toolbox Forum: open-discussion

How to make spharm mesh without alignments

Oh Jeongseok — Fri, 17 Jan 2020 5:41:41 GMT

Hello,

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 alignments were changed.
(the picture on the left is result of SPHARM module's doing alignment)
I tried to run with using registration templetes but the results were same.

So, I want to know if it can do SPHARM mesh generation without doing align again(suppose the models are all aligned already like picture on the right)

Thank you for read this question.

Regards,
Jeongseok
-----------------------------------

I just noticed there are discourse forum instead of here.
The same question is there, so please don't care about this question :)

RE: What do each of the output files represent?

Beatriz Paniagua — Tue, 10 Sep 2019 14:42:20 GMT

Hi Yash,

I would recommend having a look into our newest tutorials that describe that: https://docs.google.com/presentation/d/1ZZ6UpONwTl_GKk66Kde9Brq0PIDujw2pKavm1RD1SBo/present?slide=id.p1

Thank you,
Beatriz

ps. We have moved our user support to discourse, here is the forum where to ask questions: https://discourse.slicer.org/c/community/slicer-salt

What do each of the output files represent?

Yash Taneja — Mon, 09 Sep 2019 18:50:44 GMT

Hello,

I have inputted data through the SPHARM PDM using Slicer version 4.8.1 and have received the following output files after the ParaToSPHARMMesh step:

para.vtk
paraMix
paraPhi
paraPhiHalf
paraTheta
SPHARM.coef
SPHARM.vtk
SPHARM_ellalign.coef
SPHARMMedialAxis.vtk

What all can be done quantitatively using these outputs? And is it possible to add a distance map comparing an overlay?

Any help is appreciated, thank you!
Yash

RE: Why my paratospharmmesh folder is empty?

Beatriz Paniagua — Tue, 05 Feb 2019 13:27:46 GMT

HI Damien,

Thank you for your note. We have moved our user-support to discourse.
There is an open thread that is looking at this problem at https://discourse.slicer.org/t/paratospharmmesh-completed-with-errors-on-win10/4814/9
Thank you,
Beatriz

Why my paratospharmmesh folder is empty?

natsunami — Tue, 05 Feb 2019 12:59:07 GMT

Hi everyone !

I would like to understand why my 'paratospharmmesh' folder is empty after completing the shape analysis module ( I only have files into 'SegPostProcess' and 'GenParaMesh'. Indeed, at the end of the pipeline, when the module stop running, it says that "ParaToSPHARMMesh completed with errors" at step 2:

Widget: Running ShapeAnalysisModule
-- Scheduled : ShapeAnalysisModule
2 case(s) found
-- Running : ShapeAnalysisModule
-- Scheduled: Case 0: sub01_eb110475_meanhippoleft.nii_rsfmrires.nii.gz_binarized.nii.gz
-- Scheduled : Case 0: sub01_eb110475_meanhippoleft - step 0: SegPostProcess
-- Running : Case 0: sub01_eb110475_meanhippoleft - step 0: SegPostProcess
-- Completed : Case 0: sub01_eb110475_meanhippoleft - step 0: SegPostProcess
-- Scheduled : Case 0: sub01_eb110475_meanhippoleft - step 1: GenParaMesh
-- Running : Case 0: sub01_eb110475_meanhippoleft - step 1: GenParaMesh
-- Completing : Case 0: sub01_eb110475_meanhippoleft - step 1: GenParaMesh
-- Completed : Case 0: sub01_eb110475_meanhippoleft - step 1: GenParaMesh
-- Scheduled : Case 0: sub01_eb110475_meanhippoleft - step 2: ParaToSPHARMMesh
-- Running : Case 0: sub01_eb110475_meanhippoleft - step 2: ParaToSPHARMMesh
-- Completed with errors : Case 0: sub01_eb110475_meanhippoleft - step 2: ParaToSPHARMMesh
Saving sub01_eb110475_meanhippoleft_pp.nrrd in C:/Users/Damien/Downloads/SPHARM_Tutorial_Data_July2015/Hippo tests/outputdata/Step1_SegPostProcess
Saving sub01_eb110475_meanhippoleft_pp_para.vtk in C:/Users/Damien/Downloads/SPHARM_Tutorial_Data_July2015/Hippo tests/outputdata/Step2_GenParaMesh
Saving sub01_eb110475_meanhippoleft_pp_surf.vtk in C:/Users/Damien/Downloads/SPHARM_Tutorial_Data_July2015/Hippo tests/outputdata/Step2_GenParaMesh
-- Completed with errors: Case 0: sub01_eb110475_meanhippoleft.nii_rsfmrires.nii.gz_binarized.nii.gz
Case 0 (sub01_eb110475_meanhippoleft.nii_rsfmrires.nii.gz_binarized.nii.gz) took 9 sec to run
Case 0: sub01_eb110475_meanhippoleft - step 2: ParaToSPHARMMesh completed with errors
-- Scheduled: Case 1: sub01_eb110475_meanhipporight.nii
-- Scheduled : Case 1: sub01_eb110475_meanhipporight - step 0: SegPostProcess
-- Running : Case 1: sub01_eb110475_meanhipporight - step 0: SegPostProcess
-- Completed : Case 1: sub01_eb110475_meanhipporight - step 0: SegPostProcess
-- Scheduled : Case 1: sub01_eb110475_meanhipporight - step 1: GenParaMesh
-- Running : Case 1: sub01_eb110475_meanhipporight - step 1: GenParaMesh
-- Completing : Case 1: sub01_eb110475_meanhipporight - step 1: GenParaMesh
-- Completed : Case 1: sub01_eb110475_meanhipporight - step 1: GenParaMesh
-- Scheduled : Case 1: sub01_eb110475_meanhipporight - step 2: ParaToSPHARMMesh
-- Running : Case 1: sub01_eb110475_meanhipporight - step 2: ParaToSPHARMMesh
-- Completed with errors : Case 1: sub01_eb110475_meanhipporight - step 2: ParaToSPHARMMesh
Saving sub01_eb110475_meanhipporight_pp.nrrd in C:/Users/Damien/Downloads/SPHARM_Tutorial_Data_July2015/Hippo tests/outputdata/Step1_SegPostProcess
Saving sub01_eb110475_meanhipporight_pp_para.vtk in C:/Users/Damien/Downloads/SPHARM_Tutorial_Data_July2015/Hippo tests/outputdata/Step2_GenParaMesh
Saving sub01_eb110475_meanhipporight_pp_surf.vtk in C:/Users/Damien/Downloads/SPHARM_Tutorial_Data_July2015/Hippo tests/outputdata/Step2_GenParaMesh
-- Completed with errors: Case 1: sub01_eb110475_meanhipporight.nii
Case 1 (sub01_eb110475_meanhipporight.nii) took 91 sec to run
Case 1: sub01_eb110475_meanhipporight - step 2: ParaToSPHARMMesh completed with errors
All pipelines took: 103 sec to run
-- Completed with errors : ShapeAnalysisModule
Case 1: sub01_eb110475_meanhipporight - step 2: ParaToSPHARMMesh completed with errors

You will find attached to this message a log messages .txt,

Regards,
Damien

RE: Extension does not download

Beatriz Paniagua — Thu, 25 Oct 2018 18:49:52 GMT

HI Claire,

Thank you for your note. We have moved our user-support to discourse.
Could you please post your question at https://discourse.slicer.org/c/community/slicer-salt ?

Thank you,
Beatriz

Extension does not download

Claire Walsh — Thu, 25 Oct 2018 18:23:59 GMT

Hi I am trying to download the SPHARM-PDM extension and every time I do, it gets to 96% downloaded and then just hangs. I am using slicer 4.10.0 on a windows 7 operating system.

RE: How to perform group analysis after getting the data form SPHARM-PDM 3D-slicer4.8 in MCA_OS

Beatriz Paniagua — Tue, 19 Jun 2018 20:15:28 GMT

Hi Kailiang,

Thank you for using SPHARM! SPHARM-PDM is currently being maintained as part of SlicerSALT.
Do you mind posting your question on the SlicerSALT forum? https://discourse.slicer.org/c/community/slicer-salt

Thank you!
Beatriz

How to perform group analysis after getting the data form SPHARM-PDM 3D-slicer4.8 in MCA_OS

kailiang wang — Tue, 19 Jun 2018 18:14:30 GMT

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 know what to do! Can you help me! I am beginner to SPHARM-PDM in MCA_OS. Many thanks in advance!

RE: Where are the actual spherical harmonics coefficients?

Nazanin M — Fri, 02 Mar 2018 4:00:35 GMT

I also have the same question, and would appreciate the response.

Thanks in advance!