Hello,
I am having difficulty aligning my oblique EPIs to my anatomical data set (a Siemens sagittal MPRAGE). My EPIs are not whole brain: they are a 19-slice slab.
I have rotated my anatomical data set by the angle of rotation (recorded from the scanning session, not extracted from the dicom file) using 3drotate and attempted to align the EPIs to the anatomical data set with 3dAnatNudge.
I ran through several iterations (the max in my script was 50, but it usually settled after 10-15) of 3dAnatNudge, and it was unable to correctly align the EPIs to the anatomical image. Can 3dAnatNudge handle functional data that is not whole brain? If not, do you have any suggestions on how I can align my EPIs to my anatomical data set?
Thank you,
Kim