Gwen,
Thank you for your reply. I have generated the FA image. Since FA is
skull-stripped, should the T1 image also be skull-stripped even though fnirt
works better for the non-betted images? Also, could you clarify what do you
mean by default settings? The configuration files that are provided with the
FSL 4.1 package allow registration to a standard template, not a
user-specified brain, thus changes should be made to the given configuration
files.
Sincerely,
Anastasia
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