# 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