I would like to use AFINI for both segmentation and resting state analyses. While I’m not familiar with AFNI, it is clear that it is well suited to resting state analyses. But I don’t know if subcortical segmentation (and hence volume estimation) is possible.

I need to be able to run a two phase analysis with segmentation first followed by resting state analysis. The segmentation is aimed at testing reproducibility of volume loss (atrophy) calculation.

Two same-subject (within-subject) scans were taken at baseline only minutes apart, then 2 additional T1 scans of the same subject were take 24 months later. To assess reproducibility of volume change (PVC), derived from segmentation, say of the hippocampus, we will simply take the difference between each pair of within-subject scans:

PVC1= Volume_basline_a - Volume_24months_a/Volume_baseline_a;

PVC2= Volume_basline_b - Volume_24months_b/Volume_baseline_b;

Then median (PVC1- PVC2); closer to zero means higher reproducibility

Any feedback would be much appreciated.