Hi Mark,
I have followed your suggested and managed to get useable segmentation results (tissue+skull) as input to b0calc. However, I am stuck at the point of applying the script epi_reg. May I know what are the equivalent values to use for the following parameters, which are all required when using a fieldmap for EPI correction?
--fmapmag=<image> : fieldmap magnitude image - wholehead extracted
--fmapmagbrain=<image> : fieldmap magnitude image - brain extracted
--echospacing=<val> : Effective EPI echo spacing (sometimes called dwell time) - in seconds
--pedir=<dir> : phase encoding direction, dir = x/y/z/-x/-y/-z
--weight=<image> : weighting image (in T1 space)
Cheers,
Louis.
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