I am doing manual tracing on some T1 images. I've used flirt to align them
by registering the stripped T1 to the MNI template, and then applying the
transform back onto the unstripped image.
I've noticed that doing this changes the pixel intensities. Since I also
want to segment these brains using FAST, I was wondering if you could tell
a - exactly why do the pixel intensities change?
b - does this introduce some error when I last segment with FAST?
Basically, if I trace regions on the unsegmented image, and then attempt
to segment the grey matter within the ROI using fast will this be an
adequate representation of the region's grey matter volume?
Thanks for your help,