# use BET to get a brain mask from mag
bet mag mag_stripped -m

# prepare phase map by subtracting out mean, and converting to radians
# that odt flag on the end is important, otherwise you get integer output 
# and a useless phase map
fslmaths ph -sub 2048 -mul 3.1415927 -div 2048 ph_rad -odt float

# use PRELUDE to unwrap phase map, with mag_stripped as a mask
prelude -p ph_rad -a mag_stripped -m mag_stripped_mask -o ph_rad_unwrapped

# convert to freq. map (rad / ms, for convenience)
# delta TE for the fieldmap sequence is 2.46 ms
fslmaths ph_rad_unwrapped -div 1.02 ph_rad_per_ms

# now apply field map to data.  Need to know echo spacing
# (time for one read-out line).  FSl calls this dwell time
# which is a decidedly odd use of the term. Also need to know
# phase encode direction, which in this case was posterior -> anterior
fugue -i run01_wedge --loadfmap=ph_rad_per_ms --dwell=0.28 --nocheck --unwarpdir=y -u run01_unwarped