Hi,
I am trying to use reg-feat2anat to register my Feat analyses to anatomical images and running into a number of problems.
1) When I check the registration of the mean_func to the anatomical in tkregister2 it looks fine. But when I overlay the fsl statmaps onto the anatomical brain they extend outside of boundaries of the anatomical brain.
2) Also, before using reg-feat2anat. I was trying to do the EPI_2_structural registration in FLIRT with the fsl.mat produced by BBR. When I try this the registered image is rotated 90 degrees from the original image. Why does that happen?
3) I also noticed that if I look at the header information for an image in fslhd and mri_info the orientations are flipped. If the fslhd orientation is RAS it will be LPI in mri_info. Could this be related to what is happening in question (2)?
Best, Noam