Hi,

I am doing all of my analysis in AFNI, but 'outsource' the co-registration to FSL using FLIRT. I know that this is not a support center for FSL, but bear with me and you'll see that I have an AFNI question at the end.

I have a T2 and Mean IRF images generated by AFNI as part of an event-related design; these were all acquired in the same session. I also have a T1 that was acquired in a separate session. All images are in NIFTI format.

For the co-registration, I want to register the T2 to the T1 and then use the resulting matrix to help bring the IRFs into alignment with the T1. The T2 to T1 co-registration goes great, it's a perfect fit. However, no matter how I try to align the IRF to the T1 (through the matrix or by simply co-registering from scratch) the orientation of the image somehow gets changed. 3dinfo tells me that these image have the same orientation (RAS) as the other images, but the axial, saggital, and coronal views are different views when loaded into AFNI and the image is rotated 90 degrees in the y-plane and 180 degrees.

Are there issues with AFNI reading NIFTI headers that have been written by FSL that anyone knows of? Or are am I doing something wrong in the image managment? This seems to be the only way that I can think of such a gross misalignment.

Thank You,
Brandon