Dear AFNI Community,

Hello!! I am a newbie trying ultimately to get a cortical reconstruction of a minipig brain (with implanted microelectrode array).
Tried first in FreeSurfer but obviously the software would give an error as pig brains won't align with Talairach coordinates.

Anyway, present problem/ question:
I am following the pipeline outlined in a poster* to strip the pig skull and do segmentation before importing into FreeSurfer, but am stuck right now on the "3dWarp" step. Apparently I cannot strip the skull because the brain is "21.96 degrees from plumb" and therefore needs some "deoblique" function run on it to get it properly aligned. However, I do not really understand the syntax of the input commands (or which option commands are necessary for my particular dataset.... this is one that has been motion-corrected via 3dVolreg).

Then it seems also possibly that "3dAllineate" might be better...
The script I ran (and resulting AFNI output) is below.
Your advice or guidance will be massively appreciated!!!!!

Kind regards,
Celia




[imac-de-claire-mazzocco:Celia/150304minipig450254/T1] celiagellman% 3dSkullStrip -input r01_MC+orig.HEAD -prefix VOL_PREFIX
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./r01_MC+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./r01_MC+orig.BRIK is 21.963942 degrees from plumb.
The intensity in the output dataset is a modified version
of the intensity in the input volume.
To obtain a masked version of the input with identical values inside
the brain, you can either use 3dSkullStrip's -orig_vol option
or run the following command:
3dcalc -a r01_MC+orig.HEAD -b ./VOL_PREFIX+orig -expr 'a*step(b)' \
-prefix ./VOL_PREFIX_orig_vol
to generate a new masked version of the input.








* poster, found online, entitled "A Step-by-Step Guide to Cortical Surface Modeling of
the Nonhuman Primate Brain Using FreeSurfer" by Peggy Christidis
and Robert Cox