Dear afni experts.
I acquired a functional data that only covers the posterior part of the brain (see attached). I found it is very hard to align it to a T1 volume. I have several questions here:
1. I tried the method
here, but it did not work very well.
2. Is there any method that I can use such that I can first manually align it (I typically use itksnap or the Nudge plugin in afni), then ask align_epi_anat to fine tune it? I find that align_epi_anat has the '-pre_matrix' option which seems can achieve that. But I tried it also did not work very well.
3. I also acquired a high-resolution T2 volume. Not sure whether it can help. I am thinking of aligning T2 to T2 and then epi to T2...
Any suggestion here?
ruyuan
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