I ran the mcflirt program on the data, using the default middle volume as a
reference, and with the sbref as a reference. Both came out fine. I'm thinking
the problem lies with how FLIRT is registering each volume to the reference
image, since its registering them independently of each other.
Ho
Extract the middle timepoint using 'fslroi', and then use that as the
"Scout" (3rd argument) in the MotionCorrection_FLIRTbased.sh script.
cheers,
-MH
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Michael Harms, Ph.D.
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Conte Center for the Neuroscience of Mental Disorders
Washin
