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June 18, 2021 10:29AM
Howdy-

Just to note that AFNI's macaque demo (@Install_MACAQUE_DEMO) includes subjects who have MION during the EPI acquisition. Indeed, we found that using lpa+zz was the way to go for those, noting in the afni_proc.py part of the script:
# Using the lpa+zz cost func for some macaques who have MION;
    # lpc+zz for the others

The align block options used there were as follows:
-align_opts_aea          -cost ${cost_a2e} -giant_move                \
                                 -cmass cmass -feature_size 0.5               \
with "cost_a2e" being lpa+zz for the MION-ated macaques. Things like the need for "-giant_move" and "-cmas cmass" will be **very** dependent on how you acquire and convert your data (do you have good coords? Do you have lots of non-brain matter in the FOV? etc.). So, indeed, these kinds of things will be study-dependent.

But that makes it all the nicer to:
+ share what ideas work in what contexts, to benefit other users
+ use a program like afni_proc.py where you can relatively easily tweak/adjust these things scriptically, and save them for later and/or share them widely.

--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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