Hi,<div><br></div><div>I am trying to use reg-feat2anat to register my Feat analyses to anatomical images and running into a number of problems. </div><div><br></div><div>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. </div>
<div><br></div><div>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?</div>
<div><br></div><div>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)?</div>
<div><br></div><div>Best,</div><div>Noam</div>