Hi,
I'm trying to brain extract and noise-reduce a set of T1 structural images
to get these images ready for VBM analysis in SPM2. While the process of
Brain extracting and SUSAN are going smoothly, and nicely brain-extracted
and de-noised images are being produced, I can't figure where the coordinate
system is getting modified. Immediately following Brain-Extraction the "mm"
values in FSLview on the X, Y, and Z planes are changing from the original
~-90mm to +90mm on say the X-axis, to something like 21090mm to 21170mm.
I believe this modification of the raw-coordinates may be playing into so
difficulties making a custom t1-template from these images down the road.
I'm also seeing some changes in the header files evident by using avwinfo,
in terms of the size of each dimension.
Any insight you could offer would be wonderful.
Thank you
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