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June 17, 2021 02:21PM
Hmmm, I see. This does seem to be a notable difference between monkey EPIs and human EPIs: in the human case, typically the skullstripping/automasking isn't very important, because the skull often doesn't show up much. But for monkeys, it is a much bigger feature within the FOV.

I can imagine that lpc (or lpc+ZZ) might not work here---that is when the tissue contrast in the EPI is essentially opposite from that in the anatomical. For example, T1w anatomicals have dark ventricles, and EPIs have bright ones. So you will have to explore what works... Sometimes the EPIs have contrast agents included (e.g., MION for monkeys), and that can change the relative contrast, too, so a different cost function would be necessary.

--pt
Subject Author Posted

-epi_strip in afni_proc.py for monkeys

Doughboys June 14, 2021 08:59PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 16, 2021 03:53PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 16, 2021 05:51PM

Re: -epi_strip in afni_proc.py for monkeys

Doughboys June 17, 2021 01:39PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 17, 2021 02:21PM

Re: -epi_strip in afni_proc.py for monkeys

Doughboys June 17, 2021 03:02PM

Re: -epi_strip in afni_proc.py for monkeys

Pawel June 17, 2021 03:11PM

Re: -epi_strip in afni_proc.py for monkeys

Doughboys June 17, 2021 03:32PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 18, 2021 10:29AM



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