Hello all,
Is it appropriate to use an average EPI (mean of several runs) to calculate the coregistration matrix (align_epi_anat.py -epi2anat), and then apply this single matrix to each run (using 3dAllineate)?
Or is it better to calculate a new matrix for each run separately and then perform 3dAllineate for each run?
The mean might be a good choice if there were no motion, but there almost always is some motion. We typically recommend using the min_outlier sub-brick volume. We concatenate the rigid transformation together with the affine alignment transfomation and several other transformations to put data into a final space. See the examples in afni_proc.py. For some unusual cases where we expect larger motions across runs, we can also include additional affine transformations across runs.
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