Dear Mark
Firstly, thanks for your explanation about the issues of non-linear normalization in FIRST procedure. It really help me to realize FIRST more deeply. Currently, i work with Alzheimer's disease dataset. In my experience, when i perform FIRST analysis in patients with serve hippocampus atrophy, the FIRST can't segment hippocampus very well and cover part of CSF in final segmentation results. I also tried the -3 option with run_first_all command, the results also seems not good enough for me to perform further vertex based analysis. Based on my limited knowledge about FIRST, i think the possible reasons of this finding may come from the registration procedure (linear registration seems not well enough for AD subjects) and shape model (which only include limited numbers of aging/patient population) in current FIRST analysis procedure. Am i right ?
Could you email me this script, i have highly interest to try it in AD dataset and hope to get more reliable segmentation results! Thank you !
Best !
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