Hi,
I am new to SPHARM-PDM and trying to get it going on MAC (OSX 10.9.4).

I installed the Slicer 4.4  (according to the recently posted 2015 tutorial) and  installed the extension SPHARM-PDM. However, when I look in the modules installed the "ShapeAnalysisModule" is missing. The only installed component it is showing is "SegPostProcess".

I will appreciate any help!!!
Vinod

Dear Vinod

I just checked with my Slicer 4.4 installation (OS X 10.10.4) and I was able to see everything. This may be an issue with your Mac OSX version, i.e. that the newest extension module may not support 10.9 (Maverick), but only 10.10

The NITRC version is also compiled for 10.10 and will likely not work for 10.9. We can work on a 10.9 compilation, but I am not sure how quickly one will be ready

Best regards
Martin

Hi Martin,

Thanks for  your advise. I updated my mac OS to 10.10.4 and running Slicer 4.4 and installed the extensions SPHARM_PDM and ShapePopulationViewer using extension manager but unfortunately I still have the same problem I just don't see the Shape Analysis Module in the list of installed modules. Only module it shows under Shape Analysis Tab is  "SegPostProcess" and "ShapePopulationViewer".  I am using MacPro with 12 cores and Intel Xeon E5 processor.

Please suggest some steps for trouble shooting.

Thanks,
Vinod

Hi Vinod,



Sorry for the installation troubles. We had some library issues compiling the extension for 4.4 but we thought they were already resolved.

Have you tried Slicer 4.3.1?
http://slicer.kitware.com/midas3/slicerp...


Thanks,
Beatriz

Beatriz,
Thanks for quick response!
On your recommendation I installed the Slicer 4.3.1 and after installing the Extension SPHARM-PDM I was able to see the all the four modules installed under Shape Analysis Tab. However, there is no Shape Population Viewer extension module for Slicer 4.3.1, so i am not sure how it will effect the visualization. On the other note I tried running the 2015 example data-set with 4.3.1 slicer configuration and there were errors and showing status " Completed With Errors".

Let me know your thoughts!
Best,
Vinod

Hi Vinod,



Good that SPHARM-PDM is working for the 4.3.1 release. 
Wrt the "Completed with Errors" status, have you tried to look into the Slicer Error Log? How to access the error log is described in the new tutorial (http://www.nitrc.org/docman/view.php/308...). What does the error log say? 
Also, could you verify if your csv has the right format? i.e. using commas instead of tabs for example.


Thanks,
Beatriz

Hi Beatrize,

Here is the log of the error:

ERROR: In /Users/kitware/Dashboards/Package/Slicer-431/Base/QTCLI/vtkSlicerCLIModuleLogic.cxx, line 2042
vtkSlicerCLIModuleLogic (0x13e877310): Shape Analysis Module terminated with a fault.

One thing I wanted to check is if I need to install VTK, ITK, and Xcode on my mac to runt he SPHARM_PDM.  I am not sure if that is causing the error. Let me know if you need more information. I am attaching the CSV file I am using to runt he example you posted recently.

Best,
Vinod

Hi Vinod,



Are you creating your CSV file using Windows? When I look at your csv file using a unix terminal I see a special character that indicates the end of line in WindowsOS ("^M"). I dont think SPHARM-PDM can handle those end-of-line special characters.
I corrected it in the attached csv. Could you check if the attached file works? 


Thanks,

Beatriz

Hi Beatrize,

Thanks for catching the error. I am so use to creating CSV files using excel in mac that i did not pay attention to it and it did not even show up.

Your CSV file run without any error :-).

Thanks,
Vinod