This is a new question on what was already a very long thread. It deserves to be its own thread, which I have split off here.
I have included the link to the prior thread here, so the reference still exists.
We are dealing with alignment of an epi of partial coverage and a structural also, and came across this thread (https://afni.nimh.nih.gov/afni/community/board/read.php?1,161532,161532#msg-161532). I am about to follow the suggestions written here, but I would like to get an understanding of what we should try to achieve with 3dZeropad- Could you elaborate on how we should come to the number of planes to add?
Thank you for your input.
I find in some cases that it helps to just add a margin around the volume. Some number 10 or larger has worked for me.
Thank you for your response. Would you allow me to send you the data and ask for your help on the alignment? I can not seem to get this to work…
Sent you a PM with instructions.
Peter and I took a quick look at the data, and I think we found a good solution. The EPI data has very little anatomical structure, in that CSF is not very visible as a separate bright intensity, so cost functions that rely mostly on the inverse relationship between bright intensity in EPI and low intensity in anatomical datasets don’t work well. The solution is a different cost function, of course. I usually try lpa+ZZ and/or nmi to get at least a rough alignment. Here, this worked well. The anatSS.nii.gz dataset isn’t skullstripped as well as I would hope, but it’s good enough for this affine transformation.
align_epi_anat.py -anat anatSS.nii.gz -epi myEPI.nii.gz -dset1_strip None -dset2_strip 3dAutomask -cost lpa+ZZ -suffix _test1 -epi_base 0