Dear FMRIB,
Thanks so much for the release of FSL5.0. I am in particular excited about the integration of BBR for coregistration, but don't fully understand the usage as of yet.
The BBR page suggests the use of a bias-corrected structural image as well as a segmented structural image. The FLIRT wiki page also suggests this via the epi_reg script. However, on the FLIRT wiki and command line help I do not see options for where to specify these images. Specifically:
1) Should the wholehead_T1 and brain extracted T1 specified in epi_reg be bias corrected first? Or is this done as part of the script?
2) Where does one specify the T1 segmented image in the usage of epi_reg?
3) Can you anticipate any problems in using a non-FAST T1 segmentation for #2?
Thanks for your advice as always.
Best,
Ted
PS. Totally unrelated, but I didn't see a description of how the "extended motion parameters" are derived in the new FEAT v6.0wiki. Could you advise?
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