Dear Rober Cox,
We are trying to measure Fractional Anisotropy (FA) value of splenium using diffusion tensor images. We are using SPGR for defining our region of interest (ROI).
The raw diffusion images are distorted and the distortion is more in the frontal lobe. After registration using 3dvolreg, the two sets images( SPGR and Diffusion)appear to be misaligned. Considering the fact that we are trying to define ROI on the splenium using SPGR, even minimal misalignment can decrease the FA value estimates due to inclusion of either ventricle or gray matter.
We constructed the AFNI datasets using MRI coordinates from the scanner.
The diffusion images have 21 slices in 23 directions. b value =1000

Regards,
AMOL