DeCAL: groupwise analysis

Community SlicerMorph
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1

Dear all,

I would like to analyse two groups of skull-data, micro-CT data.

The idea is to start with group1

  • run DeCAL with the data of group1, use the models and fixed LMs to generate an atlas and the alignedLMs (group1)

Next, repeat the DeCAL with the data of group2, use the models and fixed LMs to generate an atlas and the alignedLMs (group2)

Now use DeCA to analyse group1 & group2

  • load atlas of group1
  • perform “Shape analysis”
  • model directory: folder of the alingedModels of group2
  • landmark directory: folder of the alingedLMs of group2

I guess, important would be to merge the “fixed” and the “SemiLMs” as descripted
in the tutorial.

The idea is to create an atlas based on group1. Next, to analyse “shape variances” between the atlas (group1) and each individual data set of group2. And, to analyse shape differences between the atlas1 and atlas2.

This approach is motivated by the fact that group1 varies in shape in comparison to group2, and therefor the atlas should be derived only from the data of group1.

Is such an analysis feasable with DeCA and DeCAL? And what are the important steps?

Thanks for your support.

Best,
Markus

2

This can be done in DeCAL and SLicerMorph up to a point. But there are couple important things to consider.

  1. Why are you building two atlases separately? This will create a headache for you, since during the dense semiLM creation there is no guarantee that it will create identical number of points for both groups, and if the point number and distribution is not identical, you cannot do a landmark-based shape analysis.
  2. Instead you should build the atlas using all your samples (including group 1 and 2) and then create the semiLMs etc, and then use statistical models to find groupwise differences.
  3. Statistical models are not yet available in SlicerMorph, but we do have a proposal to develop that. Until then you can migrate your data into R and then conduct the statistical analysis of group wise differences there.
1 Like
3

Dear Murat,

thanks a lot for your response and the detailed insights!

Headache,… hmmm… should be avoided :slight_smile:

Will stick to your advise!

Best,
Markus