help > new to SPHARM - some basic questions
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Jun 1, 2015  11:06 AM | Lara Foland-Ross - Stanford University
new to SPHARM - some basic questions
Hi SPHARM experts, 

I'm new to SPHARM and will be running a shape analysis of manually traced hippocampi using this software. 

I have some rather basic questions that I'm hopeful the community can shed light on:

1. should I use (a) the shape module extension from slicer or (b) spharm launched via matlab?
2. what is the most up-to-date tutorial available? Like other users, I have faced inconsistencies between the most recent release of the software and the tutorials that are documented online. I'm currently running matlab2012b on a mac.

I'm also experiencing some trouble finding documentation that instructs the user how to convert nii files to .mat and whether to load your files in native space or template space... (if the later - then with what type of registration - 6dof? more?)

Thanks very much in advance,
Lara
Jun 1, 2015  11:06 AM | Martin Styner
RE: new to SPHARM - some basic questions
All good questions.

Re 1. the most uptodate version should be available via the shape module extension, so I suggest to use that one. The SPHARM-Mat matlab software is actually a different implementation of SPHARM (by Li Shen). Our tools should work with his tools quite well, but I have no looked into Li's code in a long while.

Re 2. most are a bit out of date and we should definitely create an updated version. 
The link below describes all the command line tools and their output, though clearly is not a good tutorial
https://www.nitrc.org/plugins/mwiki/inde...

The ShapeAnalysisModule tutorial (under Docs => Documentation) relates mainly to an extension of spharm to use ShapeWorks. But that tutorial is probably the best, just disregards anything to do with Particles/ShapeWorks.

Regarding data conversion: Nifti data should work directly with Spharm, no need to convert them. 

Regarding native vs template space: SPHARM computes alignment independent of any prior alignment, so template space is not necessary, but also perfectly okay to use. In our studies we commonly have the data aligned to MNI template space with rigid registration/6DOF. Any correction for size is done during the statistical analysis (by correcting for ICV). I do not use template space data with higher DOF registration (e.g. full affine) as that will interact with the shape analysis and it makes the results harder to interpret (in my opinion).

Best regards
Martin
Jun 3, 2015  11:06 AM | Lara Foland-Ross - Stanford University
RE: new to SPHARM - some basic questions
Thanks, Martin, for your very rapid and informative response!

Just as there are many protocols for Spharm usage out there, I also see that there are multiple versions of installation instructions. Would be very grateful for some clarification on this front as well. I have a mac (osx 10.8) with slicer ver 4.4 installed. Here's my order of steps:

1. downloaded spharm as spharm-pdm_v1.13_macos.zip. Moved unzipped folder to permanent location. Added path to these files in my .bashrc file, as well as pointed to these files from slicer in order to create the "Shape Analysis Module"

2. downloaded Shape Population Viewer ver 1.3.2. Again moved files to permanent location and added path in my .bashrc file

Do I also need to download and install BatchMake? Are there other steps that I'm missing?

Thanks again!
Lara
Jun 4, 2015  06:06 AM | Martin Styner
RE: new to SPHARM - some basic questions
You do not need to install BatchMake on the newest versions. But it needs the BatchMake bmm files (to run ShapeAnalysisModule) and I realized that these were not part of the latest release. I added them to the download section as a separate download. With these, you should be able to run everything.

Best regards
Martin
Jun 4, 2015  08:06 AM | Lara Foland-Ross - Stanford University
RE: new to SPHARM - some basic questions
Thanks very much!

Lara
Oct 9, 2015  06:10 AM | Jesy Leandro Garzon Nieto - Universidad Politecnica de Madrid
RE: new to SPHARM - some basic questions
Hi SPHARM experts.

I'm new in SHRAM and I am trying to diagnose Alzheimer Disease with the hippocampi's rugosity as biomarker. Once you have obtained the rendered image would use the transform coefficients to perform post processing by SVM as presented in the document "Hippocampi Example Data" uploaded since 2010.

If I could give more information on the software used and the method that has been followed for the identification of patients I will be grateful.

Thanks in advance.
Jesy
Oct 9, 2015  06:10 AM | Beatriz Paniagua
RE: new to SPHARM - some basic questions
Hi Jesy,



Welcome to the SPHARM community. The project you explain sounds very interesting, but I have not been able to understand whether you need to use SPHARM or you have used it already and want to describe the methods.

If the first, you could start by looking at our updated tutorial https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf. If the later, I suggest to start by the following paper http://www.ncbi.nlm.nih.gov/pubmed/21941375. There are also many SPHARM application papers that explain the methods and show application examples, which sometimes help our users. You can find them here http://www.ncbi.nlm.nih.gov/pubmed/?term...


I hope that helps.
Thanks,
Beatriz
Oct 11, 2015  03:10 PM | Jesy Leandro Garzon Nieto - Universidad Politecnica de Madrid
RE: new to SPHARM - some basic questions
Thank you very much Beatriz.

Best Regards
Jesy