Hi Kristen,

What is MRIcro used for, just to convert to ANALYZE format?
The main reason NIFTI exists is because ANALYZE is so bad.
If you can avoid the ANALYZE format, do so. If you cannot,
note that AFNI can write it with 3dAFNItoANALYZE.

You should ask the Amira people about being able to read and
write the NIFTI format. Then you could have AFNI write a
NIFTI dataset, which could be directly imported into Amira,
the output of which could be read right into AFNI.

---

Assuming you need to stick to your current method, then it
is possible that the RAI orientation of the tlrc dataset is
throwing things off (since ANALYZE may not even contain the
orientation).

Converting to either LPI or maybe RPI orientation might help.

3dresample -orient RPI -input anat+tlrc -prefix anat.rpi

- rick