Hi, every SPHARM-PDM toolbox user,
I'm a novice for SPHARM-PDM toolbox.
I've been trying to setup and run it.

However, I failed to add the extension ShapeAnalysisModule.

[OS: ubuntu 11.4(x86_32), Slicer3 v.3.6, SPHARM-PDM v.1.10
The followings are my processes...
1) First, I installed and executed Slicer3 (it works well)
2) Then, I tried to add the extension SpharAnalysisModule into Slicer3
   (1) Added the BatchMake Applications by "export BatchMakeShapeAnalysisModule_Dir=/home/spharm-pdm_Linux32/bin/BatchMake_Applications".
   (2) Added the external applications by "export PATH=/home/spharm-pdm_Linux32/:${PATH}".
   (3) Added ShapeAnalysisModule as Slicer3 external module by "add a preset" in Slicer3.
   (4) Tried to add the extension ShapeAnalysisModule by using "Extension Manger menu".
        - I checked "Find & Install"
        - Change extensions install path: use the default path
        - Where to serarch: use the default path

I failed at (4) process. because there aren't any response "next button pressing".
I think there is a problem to find and install SPHARM-PDM extension.

Can anybody give extra explanation or tips to overcome the above situation?

Best regards,

Hi Jeongsik,


We are currently working in implementing ShapeAnalysisModule as a Slicer extension, however that work is not complete atm. You will have to add ShapeAnalysisModule as an external module (as described in the tutorial that can be found in the Docs section):







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The rest of the steps you follow are ok.
Let us know how can further assist you.


Regards,
BEATRIZ

Hello,

How can I add shape analysis module in slicer 4?
There is no "View → Application Settings → Module Settings" in slicer 4.
I tried "Edit→Application Settings → Module" and I added  /usr/local/bin/spharm to "Additional module path" , but it didn't work and just SegPostProcess was added.


Thanks in advance for your help,
Mahsa

Hi Mahsa, 


This is a known issue that is being investigated.
The libraries that allow to see the modules loaded in Slicer have a problem that we are tracking down. 
That happens in Linux, but not in Mac. What is your operating system?


Best,

Beatriz

Hi Beatriz,

Thanks for your reply,

My operating system is Ubuntu 12.04 LTS.

Hello,

Is there any version of slicer which has no problem with ubuntu ?
I tried slicer 3.6, but it still has the same problem and I can not add ShapeAnalysisModule.

Hi Mahsa,


Regretfully this is a problem coming from Slicer libraries that we are trying to resolve altogether with the slicer community.
Keep an eye out for updates.

Thank you!


Beatriz

Hello,

I've got a Mac and I have installed ubuntu 12.04 LTS on a virtual box,
Unfortunately, adding shape analysis module in Slicer 3D has the same problem as before!



I tried running ShapeAnalysisModule from terminal using the following command: 

./ShapeAnalysisModule --sx 0.5 --sy 0.5 --sz 0.5 --label 1 --NumberofIterations 10 --SubdivLevelValue 10 --SPHARMDegreeValue 15 --columVolumeFile 0 --varX 10 --varY 10 --varZ 10 --regTemplate None --flipTemplate None --paraOutTemplate --noFlip --HorizontalGridPara 1 --VerticalGridPara 2 --DoParticlesCorrespondence --UseProcalign ~/database/spharm_database/ShapeAnalysisModule_TutorialData/InputFile_ShapeAnalaysis_4data_.csv ~/database/spharm_database/ShapeAnalysisModule_TutorialData

but I got the following error:

------ Shape Analysis Module start -----

Computing ShapeAnalysisModule...
~/database/spharm_database/ShapeAnalysisModule_TutorialData
~/database/spharm_database/ShapeAnalysisModule_TutorialData/
~/database/spharm_database/ShapeAnalysisModule_TutorialData/ShapeAnalysisModule.bms
~/database/spharm_database/ShapeAnalysisModule_TutorialData/ShapeAnalysisModule.bms
Number of Datas: 4
Executing BatchMake...
Applications directory: ./BatchMake_Applications// doesn't exist
Error (74): 'SetApp() cannot find the application: SegPostProcessCLP
Error (93): 'SetApp() cannot find the application: GenParaMeshCLP
Error (119): 'SetApp() cannot find the application: ParaToSPHARMMeshCLP
Error (171): 'SetApp() cannot find the application: ParaToSPHARMMeshCLP
Executing BatchMake: Error!
Executing BatchMake: Done!

Maybe ShapeAnalysisModule worked well in previous versions of spharm-pdm. As I really need to use this analysis in my research, could you please tell me  in which version of spharm-pdm ShapeAnalysisModule worked well in Mac?


Thanks,
Mahsa

Hello Mahsa,


Two comments to your post.

1) When I said, Slicer integration of SPHARM works on Mac, I meant you will have to compile the tools in Mac. By creating a VirtualBox you are creating the same environment that by having a PC with Ubuntu installed.

2) For the command line execution, did you create the env variables described in the SPHARM tutorial in the Docs section of this page? 


Thank you for your feedback!

Beatriz

Thanks for the reply,

1. As the Mac version has not been updated and there was only an installation guide for Ubuntu, I thought maybe that was what you meant.
I added MacOSx.10.5.8 to slicer4. There shouldn't be Shape Analysis Module , right?
In modules I have:
Shape Analysis>GenParaMesh & ParaToSPHARMMesh & SegPostProcess
UNC>KWShapeAnalysisTool

2. In ubuntu :
I tried to do the exact steps as described in "Installing SPHARM on a fresh Ubuntu 10.10 Installation" document.
To add env variables :
cd
gedit .bashrc
#Then I added the following lines to .bashrc file:
export BatchmakeShapeAnalysisModule_Dir=/usr/local/bin/spharm/BatchMake_Applications
export PATH=/usr/local/bin/spharm/:${PATH}
But I get the following error as I said before :

------ Shape Analysis Module start-----
ComputingShapeAnalysisModule...
~/database/spharm_database/ShapeAnalysisModule_TutorialData
~/database/spharm_database/ShapeAnalysisModule_TutorialData/
~/database/spharm_database/ShapeAnalysisModule_TutorialData/ShapeAnalysisModule.bms
~/database/spharm_database/ShapeAnalysisModule_TutorialData/ShapeAnalysisModule.bms
Number of Datas: 4
Executing BatchMake...
Applications directory:./BatchMake_Applications// doesn't exist
Error (74): 'SetApp() cannot find theapplication: SegPostProcessCLP

There were some users that have been used shapeAnalysisModule in linux from terminal, is that right?

Hi Mahsa,


My advice is that you compile the source code of SPHARM for your Mac. The binaries released in that version are obsolete.

About the second problem you should make sure your BatchMake_Applications folder path exists.
Do "ls /usr/local/bin/spharm/BatchMake_Applications" (or whatever the content of your BatchmakeShapeAnalysisModule_Dir variable is) and see if that exists in your system.

Yes, we have had many users running our tools using linux commandline.


Good luck!
Let us know how it goes.


Beatriz

Hi Beatriz,

I could finally run shapeAnalysisModule! It finishes with out error and I have all the meshes in Mesh>SPHARM but no MRML scene has been created (the folder is empty).
but I used ..._surfSPHARM_procalign.vtk files as an input in shapeAnalysisMancova and I can see the result using KWMeshvisu.

I wanted to be sure that this is a correct way to use SPHARM-PDM pipeline.


Thanks,
Mahsa

Hi Mahsa,


Great news SPHARM is working. MRML scenes are not created anymore, we are preparing the tool for the new visualization tool we are including to the SPHARM-PDM suite. That will happen in the next months.

Yes, if shape changes are wanted, you have to use procalign meshes (that discard positioning changes) and visualization with KWMeshVisu is perfectly correct.


Congratulations in getting your data computed.
Stay tuned for new changes in the pipeline.


Regards,
Beatriz