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I have aligned all of our subjects' T1 images to the AC-PC line using AFNI after de-obliquing the images. Then if you deoblique the DWI and apply the AC-PC alignment (from the T1 header) you get a really good alignment of the DWI to the T1 (in AC-PC alignment)- and also after reorientation. So now I have these aligned images (in AFNI format), but now the bvecs files need to be adjusted to match (deobliqued and orientaiton corrected). I don't know how to apply, or in what order, or how to verify that I have done it correctly these transformations. Any suggestions? The point is to keep the images in this alignment, but then do all of the DWI processing in FSL. Thanks!