I have two low-resolution functional scans and one high-resolution anatomic
scan, all acquired on the same subject within two hours of each other, and
I'd like to align them. My analysis isn't GLM or ICA, so I'd like to
perform the alignment outside of FEAT. Currently, I'm trying the following:
1) run BET on all three scans
2) use FLIRT to align each functional scan to the anatomic as reference,
with 12 DOF, saving the resulting matrices (but not generating output data sets)
3) run MCFLIRT on each functional scan, using the -init option to include
the associated matrix generated by FLIRT
I have three questions:
1) Is this the right way to proceed?
2) Which volume does FLIRT choose when it performs the alignment to the
structural image?
3) Should I run BET before FLIRT and MCFLIRT, or after? Message #6302 seems
to suggest that in this case perhaps not.
Many thanks for a great suite of programs.
Steve
http://cordelia.mclean.org/~lowen/
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