#Example Setup File
# all lines beginning with # are ignored 
#
#
#
# List all subjects here
#
#
#
# Put reference brain here
#
set reflist {
sn184_shaywitz/sn184_3D_stripped.hdr
sn215_shaywitz/sn215_3D_stripped.hdr
sn253_shaywitz/sn253_3D_stripped.hdr
sn324_shaywitz/sn324_3D_stripped.hdr
sn361_shaywitz/sn361_3D_stripped.hdr
sn403_shaywitz/sn403_3D_stripped.hdr
sn460_shaywitz/sn460_3D_stripped.hdr
sn748_shaywitz/sn748_3D_stripped.hdr
sn782_shaywitz/sn782_3D_stripped.hdr
sn850_shaywitz/sn850_3D_stripped.hdr
sn90_shaywitz/sn90_3D_stripped.hdr
sn136_shaywitz/sn136_3D_stripped.hdr
sn138_shaywitz/sn138_3D_stripped.hdr
sn171_shaywitz/sn171_3D_stripped.hdr
sn212_shaywitz/sn212_3D_stripped.hdr
sn392_shaywitz/sn392_3D_stripped.hdr
sn424_shaywitz/sn424_3D_stripped.hdr
sn426_shaywitz/sn426_3D_stripped.hdr
sn434_shaywitz/sn434_3D_stripped.hdr
sn449_shaywitz/sn449_3D_stripped.hdr
sn479_shaywitz/sn479_3D_stripped.hdr
sn492_shaywitz/sn492_3D_stripped.hdr
sn508_shaywitz/sn508_3D_stripped.hdr
sn524_shaywitz/sn524_3D_stripped.hdr
sn528_shaywitz/sn528_3D_stripped.hdr
sn543_shaywitz/sn543_3D_stripped.hdr
sn603_shaywitz/sn603_3D_stripped.hdr
sn691_shaywitz/sn691_3D_stripped.hdr
sn703_shaywitz/sn703_3D_stripped.hdr
sn744_shaywitz/sn744_3D_stripped.hdr
sn925_shaywitz/sn925_3D_stripped.hdr
sn939_shaywitz/sn939_3D_stripped.hdr
sn958_shaywitz/sn958_3D_stripped.hdr
sn793_shaywitz/sn793_3D_stripped.hdr
sn698_shaywitz/sn698_3D_stripped.hdr
}
#
set trglist {
sn184_shaywitz/sn184_shaywitz_stack3d_S003.hdr
sn215_shaywitz/sn215_shaywitz_stack3d_S003.hdr
sn253_shaywitz/sn253_shaywitz_stack3d_S003.hdr
sn324_shaywitz/sn324_shaywitz_stack3d_S003.hdr
sn361_shaywitz/sn361_shaywitz_stack3d_S003.hdr
sn403_shaywitz/sn403_shaywitz_stack3d_S003.hdr
sn460_shaywitz/sn460_shaywitz_stack3d_S003.hdr
sn748_shaywitz/sn748_shaywitz_stack3d_S003.hdr
sn782_shaywitz/sn782_shaywitz_stack3d_S003.hdr
sn850_shaywitz/sn850_shaywitz_stack3d_S003.hdr
sn90_shaywitz/sn90_shaywitz_stack3d_S003.hdr
sn136_shaywitz/sn136_shaywitz_stack3d_S003.hdr
sn138_shaywitz/sn138_shaywitz_stack3d_S003.hdr
sn171_shaywitz/sn171_shaywitz_stack3d_S003.hdr
sn212_shaywitz/sn212_shaywitz_stack3d_S003.hdr
sn392_shaywitz/sn392_shaywitz_stack3d_S003.hdr
sn424_shaywitz/sn424_shaywitz_stack3d_S003.hdr
sn426_shaywitz/sn426_shaywitz_stack3d_S003.hdr
sn434_shaywitz/sn434_shaywitz_stack3d_S003.hdr
sn449_shaywitz/sn449_shaywitz_stack3d_S003.hdr
sn479_shaywitz/sn479_shaywitz_stack3d_S003.hdr
sn492_shaywitz/sn492_shaywitz_stack3d_S003.hdr
sn508_shaywitz/sn508_shaywitz_stack3d_S003.hdr
sn524_shaywitz/sn524_shaywitz_stack3d_S003.hdr
sn528_shaywitz/sn528_shaywitz_stack3d_S003.hdr
sn543_shaywitz/sn543_shaywitz_stack3d_S003.hdr
sn603_shaywitz/sn603_shaywitz_stack3d_S003.hdr
sn691_shaywitz/sn691_shaywitz_stack3d_S003.hdr
sn703_shaywitz/sn703_shaywitz_stack3d_S003.hdr
sn744_shaywitz/sn744_shaywitz_stack3d_S003.hdr
sn925_shaywitz/sn925_shaywitz_stack3d_S003.hdr
sn939_shaywitz/sn939_shaywitz_stack3d_S003.hdr
sn958_shaywitz/sn958_shaywitz_stack3d_S003.hdr
sn793_shaywitz/sn793_shaywitz_stack3d_S005.hdr
sn698_shaywitz/sn698_shaywitz_stack3d_S004.hdr
}
#
#
# beginsubject determines which would the first subject to be processed
# -1 = default automatically determines whether this is a new job or a restarting of a crashed job
set beginsubject -1
# mode = linear,nonliear,distortion
set mode  "rigid"
#set mode "rigid"
#set mode "affine"
#set mode "distortion"
#
#
# Tweak parameters
# filetype = 1 includes directory name in output filename 0 does not
# defaults are for rigid/affine/nonlinear
set resolution 1.5
set spacing   15.0
set iterations 15
set stepsize 1
set smoothness auto

#For Distortion Correction use
#set resolution 4.0
#set spacing   12.0
#set iterations 15
#set stepsize 4
#set smoothness 0.05
set phaseencode 1

# If in Child Study center set this to 1 otherwise leave alone
set filenametype 0