Hi,
I've been having trouble aligning a BOLD functional image to a high resolution T1 anatomical image. I'm basically using 3dAllineate. The following is the command I used.
3dAllineate -base ../0013/T1_skull_removed+tlrc -source BOLD-1_Masked+orig -prefix BOLD-1-align
For some reason, it just doesn't align properly. It is plainly obvious the the ventricles do not line up at all in any direction.
Also as a side note, does anybody know why the size of the resulting image is something along the lines of 1.3 GB? That seems rather extreme.
Thanks for any insight.