Hi Peter,
Thanks for getting back, here are some images (sorry I can never get the image upload in afni to work properly)
This is the problematic participant, P07_LV
With giant move - big fail
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photos.app.goo.gl]
With ginormous move - better but still bad
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photos.app.goo.gl]
Thanks for the link, that's where I got the idea for the nudge and 3dAllineate from - which works well for the problematic P07_LV (note the apparent misalignment at the front and back looks to be due to signal drop out, apparent when viewed at higher overlay threshold)
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photos.app.goo.gl]
This is for the other participant where I had more success
Giant move, ginormous move and nudge + giant move all produce nearly identical results (you have to really look closely to see the differences). It looks like the below. The alignment in frontal/ medial areas seems to be quite off still with these methods
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photos.app.goo.gl]
I've never had any luck using lpc+ZZ cost function in alignment with my data, they always turn out warped. Perhaps because it is partial data and I should try lpa lpa+ZZ as Daniel suggests?
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photos.app.goo.gl]
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photos.app.goo.gl]
Happy to share data if that might be helpful. Thank you for your help!
Harriet
