# mritotal.icbm.cfg
#
# This is an example protocol file for mritotal.  It works quite well
# with data acquired at the MNI according to the ICBM protocol, and is
# provided as an alternative example.  See mritotal.default.cfg for
# full instructions.

# protocol for ICBM data by Greg Ward 95/08/23


# The data is first subsampled to a regular grid, specified here as
# the voxel step size for all three spatial dimensions in mm.  ICBM
# data is acquired on a 1mm isotropic grid, so we just double the step
# size to save memory and time.

-isosubsample 2

# The data is cropped according to the three pairs of numbers supplied
# here.  Each pair specifies what to do to the data along one axis (x,
# y, z).  The two numbers tell how to extend the volume at,
# respectively, the low and high end of the axis.  Here, "low" and
# "high" refer to the real-world coordinate system specified by the
# MINC standard, ie. the low end of the x axis is the patient's left,
# low y is patient posterior, and low z is patient inferior.  In this
# case, we leave the x and y axes alone, and chop off 25% of the data
# at the bottom of the scan.  This is because ICBM MRI data extends
# well down into the neck, and we need to discard this excess data
# because we're only interested in fitting brains.

-crop 0,0 0,0 -25%,0

# Specify the objective function used for fitting.  

-objective xcorr