Hi,

My interest is in cortical thickness measurements for longitudinal Alzheimer data, namely the ADNI dataset.

My understanding is that recon-all can be used to generate cortical thicknesses.

I am trying to understand how the default parameter values used in recon-all were arrived at.

Are the default parameters optimized in some sense?

How robust are the default parameters with respect to the resulting cortical thickness?

Will a small change in a parameter value result in a significant difference in some cortical thicknesses?

I was able to find the following and would appreciate references to good papers on this topic.

Excerpt from abstract:

Standard manual tracing and FreeSurfer-based analyses were performed in 77 participants including 67 cognitively normal individuals and 10 individuals with early Alzheimer's disease….

The manual and FreeSurfer approaches yielded nearly identical estimates of amyloid burden (intraclass correlation = 0.98) as assessed by the mean cortical binding potential.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0073377

Thanks for any forthcoming comments.

Mark