Re: partial coverage alignment

AFNI Message Board
1

Hi-

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.

–pt

Hello-

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.

Nobuko

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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.

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Dear Peter,

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…

Nobuko

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Sent you a PM with instructions.

5

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

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Thank you so much!

Nobuko