Hi, Fabian-
That centering looks like a *much* better place to start the alignment. I wouldn't worry about any differences from here-- the alignment procedure will (or should) take care of those. The purpose of this is to just have the datasets starting in a reasonably close overlap, which they certainly appear to have now.
Re. cropping-- yes, you can do this in AFNI. NOooooooooooooooo need to use matlab, yikes... 3dZeropad can be used to place extra slices of zeros around a volume, *or* to remove slices from sides of the volume (basically, providing negative values for how much padding to do):
[
afni.nimh.nih.gov]
At this point for your dset, it might be useful just to greatly reduce the size of files and subsequent processing time. That is assuming, of course, you don't need the "outside brain" parts of the macaque for further processing? (e.g., positioning electrodes on outer part of scalp?) You list some interesting projects for this dataset, but I am not familiar with them with any personal experience.
For example, to remove extra inf/sup slices, you could try to remove 40 from the "top" and 50 from the "bottom":
3dZeropad \
-I -50 \
-S -40 \
-prefix T1w_recent_crop.nii.gz \
T1w_recent.nii.gz
... and I am tooootally guessing at values for how much you could remove. Please visually check that it isn't too much! And you can remove slices along other axes in a similar way.
And one last thing-- I will put in another plug for using NMT v2.0, esp. the 0.5mm resolution version, for all the reasons suggested in the previous message.
--pt
