Hi FSL group,
I want to transform ROIs from the AAL atlas to my subjects onto their T1s. But when I try to do this the ROIs are not in the proper location. My command is below:
flirt -in AAL_71 -ref T1 -applyxfm -out left_caudate -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -applyxfm -usesqform -interp trilinear
Another (potential) complication that may be the cause is that my subjects consists of controls and 2 patient groups that have a lot of degeneration.
Your help would be greatly appreciated!!
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