Hello,
  

  ı downloaded the zip file v.1.10.7 : spharm-pdm_v1.10_linux32.zip. Is that version has a interface ?
  if it has , how can ı start the interface?

  Any help would be greatly appreciated. Thanks !
 
   Onur.

Hi Onur,

The module ShapeAnalysisModule is a Slicer interface. That is to say you have toad the directories of the binaries in Slicer3.
The second part, ShapeAnalysisMANCOVA is a graphic interface loadable via Slicer or via command line.
You can find a tutorial of shapeAnalysisModule in Docs/Documentation and for the MANCOVA module at the same place but on this page : http://www.nitrc.org/projects/shape_mancova/.

Let us know if you have any kind of issues.

Best regards,
Lucile

Hi Lucile , Thanks for response.

 ı began to work in command line. I applied to hipocampus this three procedure.

 1)SegPostProcess 

 2)GenParaMesh 

 3)ParaToSPHARMMesh  

   And the outputs are ;
label_surfSPHARM.coef,
label_surfSPHARM.meta,
label_surfSPHARM_ellalign.coef,
label_surfSPHARM_ellalign.meta and
label_surfSPHARM_procalign.meta. 

 How can ı use that data for statistical analysis ?  
 
 Any help would be greatly appreciate. Thanks!

 Onur

Hi Onur,

Can you show me how you were able to obtain the outputs through the command line for the Hippocampus data set? Is the processed data for the entire group of hippocampi? Using the Slicer interface, I can't seem to generate those outputs without errors. I'd greatly appreciate it.

Thanks!
Sylvia

Hi Onur,

Yes indeed, you can use those files for the statistical study.
You can go on this page : http://www.nitrc.org/projects/shape_mancova/

And then you can follow the tutorial.
Let me know if you have any kind of questions.

Best Regards,
Lucile

ı have been already trying to use shapeAnalysis_MANCOVA. Because of not using the shapeanalysismodule , ı couldnt create a csv file for shapeAnalysis_MANCOVA. As ı told in previous message, ı have these files ; label_surfSPHARM.coef, label_surfSPHARM.meta,

label_surfSPHARM_ellalign.coef,  label_surfSPHARM_ellalign.meta and

label_surfSPHARM_procalign.meta.
 ı discovered that csv file should contain vtk files path. But ı havent got vtk files. Can I use the label_surfSPHARM_procalign.meta.for csv file after converting with way of "Meta2VTK".
 
 Thanks.
 Onur...

Hi Sylvia,

I followed these step in SPHARM-PDM Insight Journal 2006. I used terninal for process. The article involves the use of functions.
 
 You can reach the article by http://www.nitrc.org/docman/index.php?gr...

 I hope it will helpful for you. İf there is a problem afterwords you can write again.

 Onur...

Hi Onur,

The article was very helpful with the command lines, thank you. I have a few questions, hopefully you can answer them since you were able to work through the main pipeline.

1. What is the number you put for --label for SegPostProcess and GenParaMesh? For the given hippocampus tutorial data set, I noticed that if I put --label 1, the output is an empty image, and if I leave the --label out using the default value of 0, I actually get a volume image. However, when I apply --label 0 using the output binary file from SegPostProcess for GenParaMesh, an error occur.

2. For GenParaMesh, do you only get two mesh outputs: _para.meta and _surf.meta ?

3. In the article, for ParaToSPHARMMesh, they have filenames for flipTemplate and regTemplate. Where would I usually find the .coef and .meta file for those inputs?

Thank you,
Sylvia

Hi Sylvia, 
 
I'am so sorry, ı forgot to response your questions.

 1. I have wrote my pipeline in http://www.nitrc.org/forum/forum.php?thread_id=2525&forum_id=1281 .
 
 2. yes.

 3. http://www.nitrc.org/forum/forum.php?thread_id=2525&forum_id=1281

 I hope , thats help. I sorry about the late response. 

 Regards,

 Onur...