NITRC SPHARM-PDM Toolbox Forum: help

shapeAnalysisMANCOVA_Wizard error

Han Zhuang — Sun, 21 Oct 2018 16:07:33 GMT

Dear experts:

I add spharm-pdm_v1.11_linux64 as an extension to 3D Slicer4.8.1. The statistics->shapeAnalysisMANCOVA_Wizard module can be found in the Modules drop-down menu.We can successfully open the shapeAnalysisMANCOVA_Wizard graphical interface. But when we load the *.csv data, it will flash back and then it will report an error.
Error message :
ShapeAnalysisMANCOVA_Wizard standard error: / home/imewsq/spharm - pdm_v1. 11 _linux64 / shapeAnalysisMANCOVA_Wizard: symbol lookup error: / home/imewsq/spharm - pdm_v1. 11 _linux64 / shapeAnalysisMANCOVA_Wizard:Undefined symbol: _ZNK7QString12ascii_helperEv

I don't know how to solve it. Can you help me! I am beginner to shapeAnalysisMANCOVA_Wizard in Linux .

Many thanks in advance!

RE: Why flip patterns are only 7??

Beatriz Paniagua — Fri, 18 May 2018 17:11:08 GMT

Hi,

Thank you for using SPHARM. Could you please post this question in our new forum at https://discourse.slicer.org/c/community/slicer-salt
Best regards,

Beatriz

Why flip patterns are only 7??

yfujii08 — Mon, 14 May 2018 23:15:54 GMT

In your script in ParametricMeshToSPHARMSpatialObjectFliter.cxx,
you flip coef in 7 patterns using flip_fu[0-2|reflect] functions.
Is there any mathematical proof of necessary and sufficient condition?
If it exist, I would appreciate if you let me know the reference.

RE: Problems running SPHARM-PDM tool

Beatriz Paniagua — Mon, 07 May 2018 13:15:52 GMT

Hi Pilar,

Could you post this question in the new https://discourse.slicer.org/c/community/slicer-salt forum?
Thank you!

Beatriz

Problems running SPHARM-PDM tool

Pilar Espana — Mon, 07 May 2018 11:35:14 GMT

Hello users,

I am having problems using the SPHARM-PDM module. I read the user tutorial (May 2017) but when I apply the module, the status says completed with errors.

The purpose of my PhD is to make the comparison between two hemi-mandibles (right and left) and find if there is any asymmetry (quantifying the distance between every correspondent point).
After doing all the previous steps, and using a voxel-based registration, I get the volume (.vtk) of each one and then I create a new file with the module Model to Model distance, getting the colormap file (.vtk).

I try to do the SPHARM-PDM analysis with this file (colormap) to do the statistics in a simpler way, but I have errors. Probably it is because I am not clicking or selecting the correct parameters.

I attach a file to show what I do.

Looking forward to hearing from you.

Thank you in advance

RE: SPHARM-PDM on 3D Slicer error: Shape Analysis Module terminated with a fault.

Beatriz Paniagua — Tue, 19 Dec 2017 14:29:17 GMT

Hi Soda,

Thanks for your question. We have migrated our forums to Discourse, could you please post your question here? https://discourse.slicer.org/c/community/slicer-salt
Best,

Beatriz

SPHARM-PDM on 3D Slicer error: Shape Analysis Module terminated with a fault.

soda soda — Tue, 19 Dec 2017 3:32:43 GMT

Hello, everyone! I have a problem using the SPHARM-PDM on 3D Slicer(v4.4.0).
I follow the[url=../docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf] tutorial [/url]. I changed the filepath in the .csv file like this:

Gender InputFile1 Input File Description
0 /home/soda/Downloads/SPHARM_Tutorial_Data_July2015/origData/groupA_01_hippo.gipl.gz none
0 /home/soda/Downloads/SPHARM_Tutorial_Data_July2015/origData/groupA_02_hippo.gipl.gz none
1 /home/soda/Downloads/SPHARM_Tutorial_Data_July2015/origData/groupB_01_hippo.gipl.gz none
1 /home/soda/Downloads/SPHARM_Tutorial_Data_July2015/origData/groupB_02_hippo.gipl.gz none

and set the other parameters as the tutorial said. But I got error when apply the shape analysis:

Shape Analysis Module terminated with a fault.

and here are more details:

Found CommandLine Module, target is /home/soda/.config/NA-MIC/Extensions-23774/SPHARM-PDM/lib/Slicer-4.4/cli-modules/ShapeAnalysisModule
ModuleType: CommandLineModule
Shape Analysis Module command line:
/home/soda/.config/NA-MIC/Extensions-23774/SPHARM-PDM/lib/Slicer-4.4/cli-modules/ShapeAnalysisModule --RescaleSegPostProcess --sx 0.5 --sy 0.5 --sz 0.5 --label 1 --NumberofIterations 1000 --SubdivLevelValue 10 --SPHARMDegreeValue 15 --thetaIterationValue 100 --phiIterationValue 100 --medialMesh --columVolumeFile 0 --varX 10 --varY 10 --varZ 10 --regTemplate None --flipTemplate None --paraOutTemplate --noFlip --HorizontalGridPara 5 --VerticalGridPara 5 --UseProcalign --startRegularization 10 --endRegularization 0.01 --optimizationIt 200 --RelativeWeight 1 /home/soda/Downloads/SPHARM_Tutorial_Data_July2015/origData/groupA_01_hippo.gipl.gz /home/soda/Downloads/SPHARM_Tutorial_Data_July2015/output
Shape Analysis Module standard output:
------ Shape Analysis Module start -----
Computing ShapeAnalysisModule...
/home/soda/Downloads/SPHARM_Tutorial_Data_July2015/output/
/home/soda/Downloads/SPHARM_Tutorial_Data_July2015/output/ShapeAnalysisModule.bms

Do you know how to fix it?
Thanks for your reply!

How can I move on to the surfstat?

June Kang — Sat, 14 Oct 2017 7:32:43 GMT

I proceed the SPHARM-PDM procedures, and have ellalign.vtk and ellaign.coef files.
I have to run surfstat, since I need more complex MANCOVA.

How can I change the structure of coef?

Bests,
J.

RE: SPHARM-PDM Nifti Files to gipl.gz files

Beatriz Paniagua — Wed, 12 Apr 2017 18:43:00 GMT

Glad to hear!

RE: SPHARM-PDM Nifti Files to gipl.gz files

Jacqueline Harris — Wed, 12 Apr 2017 18:28:38 GMT

Thanks for the quick reply Beatriz, seems to work now!