#
# Configuration file for mritotal.  These are just mritotal
# command-line options, with lots of comments and blank lines.
#
# There are three broad classes of configuration variables:
# site-specific (location of model, default protocol), data specific
# (preprocessing steps to take), and preferences (everything else).
# Site-specific options and preferences are found in this file;
# data-specific options are found in the protocol file, which is just
# called mritotal.foo.cfg, where "foo" is the protocol.  Thus a site
# (or user) can specify any number of protocols, either here or on the
# command line, and the last one given takes precedence.  (The command
# line is processed after this file!)
#
# Note that all of these can be overridden on the command line.
#

# ---------------------------------------------------------------
# Site-specific options -- if you edited Makefile.include to
# correctly reflect where the "average_305" stereotaxic model
# is installed on your system, these should be fine.
# ---------------------------------------------------------------

# -modeldir /usr/pubsw/packages/mni/1.4/share/mni_autoreg    # problem! however mritotal defaults handle this
-model average_305
-protocol default


# ---------------------------------------------------------------
# Other stuff - these are just personal preferences that don't
# affect the fit.  (Except -execute, which would completely
# disable fitting if you used -noexecute.)
# ---------------------------------------------------------------

-verbose			# print commands and status info
-execute			# actually execute commands
-noclobber			# do not blithely overwrite output files
-nodebug			# do not make minctracc and mincblur very noisy
-nokeeptmp			# do delete all temp files