#Example Setup File
# all lines beginning with # are ignored 
#
#
#
# List all subjects here
#
#
#
# Put reference brain here
#
set reflist {
sn698_shaywitz/sn698_shaywitz_stack3d_S004.hdr
sn793_shaywitz/sn793_shaywitz_stack3d_S005.hdr
sn2086_shaywitz/sn2086_shaywitz_stack3d_S004.hdr
sn90_shaywitz/sn90_shaywitz_stack3d_S003.hdr
sn131_shaywitz/sn131_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
sn181_shaywitz/sn181_shaywitz_stack3d_S003.hdr
sn184_shaywitz/sn184_shaywitz_stack3d_S003.hdr
sn212_shaywitz/sn212_shaywitz_stack3d_S003.hdr
sn215_shaywitz/sn215_shaywitz_stack3d_S003.hdr
sn247_shaywitz/sn247_shaywitz_stack3d_S003.hdr
sn253_shaywitz/sn253_shaywitz_stack3d_S003.hdr
sn272_shaywitz/sn272_shaywitz_stack3d_S003.hdr
sn295_shaywitz/sn295_shaywitz_stack3d_S003.hdr
sn324_shaywitz/sn324_shaywitz_stack3d_S003.hdr
sn361_shaywitz/sn361_shaywitz_stack3d_S003.hdr
sn392_shaywitz/sn392_shaywitz_stack3d_S003.hdr
sn403_shaywitz/sn403_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
sn460_shaywitz/sn460_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
sn539_shaywitz/sn539_shaywitz_stack3d_S003.hdr
sn542_shaywitz/sn542_shaywitz_stack3d_S003.hdr
sn543_shaywitz/sn543_shaywitz_stack3d_S003.hdr
sn602_shaywitz/sn602_shaywitz_stack3d_S003.hdr
sn603_shaywitz/sn603_shaywitz_stack3d_S003.hdr
sn659_shaywitz/sn659_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
sn748_shaywitz/sn748_shaywitz_stack3d_S003.hdr
sn782_shaywitz/sn782_shaywitz_stack3d_S003.hdr
sn850_shaywitz/sn850_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
sn975_shaywitz/sn975_shaywitz_stack3d_S003.hdr
sn1083_shaywitz/sn1083_shaywitz_stack3d_S003.hdr
sn1095_shaywitz/sn1095_shaywitz_stack3d_S003.hdr
sn1101_shaywitz/sn1101_shaywitz_stack3d_S003.hdr
sn1106_shaywitz/sn1106_shaywitz_stack3d_S003.hdr
sn1110_shaywitz/sn1110_shaywitz_stack3d_S003.hdr
sn1162_shaywitz/sn1162_shaywitz_stack3d_S003.hdr
sn1175_shaywitz/sn1175_shaywitz_stack3d_S003.hdr
sn1288_shaywitz/sn1288_shaywitz_stack3d_S003.hdr
sn1301_shaywitz/sn1301_shaywitz_stack3d_S003.hdr
sn1442_shaywitz/sn1442_shaywitz_stack3d_S003.hdr
sn1464_shaywitz/sn1464_shaywitz_stack3d_S003.hdr
sn1468_shaywitz/sn1468_shaywitz_stack3d_S003.hdr
sn1476_shaywitz/sn1476_shaywitz_stack3d_S003.hdr
sn1513_shaywitz/sn1513_shaywitz_stack3d_S003.hdr
sn1517_shaywitz/sn1517_shaywitz_stack3d_S003.hdr
sn1520_shaywitz/sn1520_shaywitz_stack3d_S003.hdr
sn1567_shaywitz/sn1567_shaywitz_stack3d_S003.hdr
sn1575_shaywitz/sn1575_shaywitz_stack3d_S003.hdr
sn1576_shaywitz/sn1576_shaywitz_stack3d_S003.hdr
sn1590_shaywitz/sn1590_shaywitz_stack3d_S003.hdr
sn1595_shaywitz/sn1595_shaywitz_stack3d_S003.hdr
sn1604_shaywitz/sn1604_shaywitz_stack3d_S003.hdr
sn1622_shaywitz/sn1622_shaywitz_stack3d_S003.hdr
sn1623_shaywitz/sn1623_shaywitz_stack3d_S003.hdr
sn1624_shaywitz/sn1624_shaywitz_stack3d_S003.hdr
sn1638_shaywitz/sn1638_shaywitz_stack3d_S003.hdr
sn1646_shaywitz/sn1646_shaywitz_stack3d_S003.hdr
sn1651_shaywitz/sn1651_shaywitz_stack3d_S003.hdr
sn1656_shaywitz/sn1656_shaywitz_stack3d_S003.hdr
sn1658_shaywitz/sn1658_shaywitz_stack3d_S003.hdr
sn1687_shaywitz/sn1687_shaywitz_stack3d_S003.hdr
sn1761_shaywitz/sn1761_shaywitz_stack3d_S003.hdr
sn1772_shaywitz/sn1772_shaywitz_stack3d_S003.hdr
sn1829_shaywitz/sn1829_shaywitz_stack3d_S003.hdr
sn1940_shaywitz/sn1940_shaywitz_stack3d_S003.hdr
sn2036_shaywitz/sn2036_shaywitz_stack3d_S003.hdr
sn2435_shaywitz/sn2435_shaywitz_stack3d_S003.hdr
}
#
set trglist {
sn698_shaywitz/sn698_shaywitz_stack4d_S708_020.hdr
sn793_shaywitz/sn793_shaywitz_stack4d_S709_020.hdr
sn2086_shaywitz/sn2086_shaywitz_stack4d_S708_020.hdr
sn90_shaywitz/sn90_shaywitz_stack4d_S707_020.hdr
sn131_shaywitz/sn131_shaywitz_stack4d_S707_020.hdr
sn136_shaywitz/sn136_shaywitz_stack4d_S707_020.hdr
sn138_shaywitz/sn138_shaywitz_stack4d_S708_020.hdr
sn171_shaywitz/sn171_shaywitz_stack4d_S707_020.hdr
sn181_shaywitz/sn181_shaywitz_stack4d_S707_020.hdr
sn184_shaywitz/sn184_shaywitz_stack4d_S707_020.hdr
sn212_shaywitz/sn212_shaywitz_stack4d_S707_020.hdr
sn215_shaywitz/sn215_shaywitz_stack4d_S707_020.hdr
sn247_shaywitz/sn247_shaywitz_stack4d_S707_020.hdr
sn253_shaywitz/sn253_shaywitz_stack4d_S707_020.hdr
sn272_shaywitz/sn272_shaywitz_stack4d_S707_020.hdr
sn295_shaywitz/sn295_shaywitz_stack4d_S707_020.hdr
sn324_shaywitz/sn324_shaywitz_stack4d_S707_020.hdr
sn361_shaywitz/sn361_shaywitz_stack4d_S707_020.hdr
sn392_shaywitz/sn392_shaywitz_stack4d_S707_020.hdr
sn403_shaywitz/sn403_shaywitz_stack4d_S707_020.hdr
sn424_shaywitz/sn424_shaywitz_stack4d_S707_020.hdr
sn426_shaywitz/sn426_shaywitz_stack4d_S707_020.hdr
sn434_shaywitz/sn434_shaywitz_stack4d_S707_020.hdr
sn449_shaywitz/sn449_shaywitz_stack4d_S707_020.hdr
sn460_shaywitz/sn460_shaywitz_stack4d_S707_020.hdr
sn479_shaywitz/sn479_shaywitz_stack4d_S707_020.hdr
sn492_shaywitz/sn492_shaywitz_stack4d_S707_020.hdr
sn508_shaywitz/sn508_shaywitz_stack4d_S707_020.hdr
sn524_shaywitz/sn524_shaywitz_stack4d_S707_020.hdr
sn528_shaywitz/sn528_shaywitz_stack4d_S707_020.hdr
sn539_shaywitz/sn539_shaywitz_stack4d_S707_020.hdr
sn542_shaywitz/sn542_shaywitz_stack4d_S707_020.hdr
sn543_shaywitz/sn543_shaywitz_stack4d_S707_020.hdr
sn602_shaywitz/sn602_shaywitz_stack4d_S707_020.hdr
sn603_shaywitz/sn603_shaywitz_stack4d_S707_020.hdr
sn659_shaywitz/sn659_shaywitz_stack4d_S707_020.hdr
sn691_shaywitz/sn691_shaywitz_stack4d_S707_020.hdr
sn703_shaywitz/sn703_shaywitz_stack4d_S707_020.hdr
sn744_shaywitz/sn744_shaywitz_stack4d_S707_020.hdr
sn748_shaywitz/sn748_shaywitz_stack4d_S707_020.hdr
sn782_shaywitz/sn782_shaywitz_stack4d_S707_020.hdr
sn850_shaywitz/sn850_shaywitz_stack4d_S707_020.hdr
sn925_shaywitz/sn925_shaywitz_stack4d_S707_020.hdr
sn939_shaywitz/sn939_shaywitz_stack4d_S707_020.hdr
sn958_shaywitz/sn958_shaywitz_stack4d_S707_020.hdr
sn975_shaywitz/sn975_shaywitz_stack4d_S707_020.hdr
sn1083_shaywitz/sn1083_shaywitz_stack4d_S707_020.hdr
sn1095_shaywitz/sn1095_shaywitz_stack4d_S707_020.hdr
sn1101_shaywitz/sn1101_shaywitz_stack4d_S707_020.hdr
sn1106_shaywitz/sn1106_shaywitz_stack4d_S707_020.hdr
sn1110_shaywitz/sn1110_shaywitz_stack4d_S707_020.hdr
sn1162_shaywitz/sn1162_shaywitz_stack4d_S707_020.hdr
sn1175_shaywitz/sn1175_shaywitz_stack4d_S707_020.hdr
sn1288_shaywitz/sn1288_shaywitz_stack4d_S707_020.hdr
sn1301_shaywitz/sn1301_shaywitz_stack4d_S707_020.hdr
sn1442_shaywitz/sn1442_shaywitz_stack4d_S707_020.hdr
sn1464_shaywitz/sn1464_shaywitz_stack4d_S707_020.hdr
sn1468_shaywitz/sn1468_shaywitz_stack4d_S707_020.hdr
sn1476_shaywitz/sn1476_shaywitz_stack4d_S707_020.hdr
sn1513_shaywitz/sn1513_shaywitz_stack4d_S707_020.hdr
sn1517_shaywitz/sn1517_shaywitz_stack4d_S707_020.hdr
sn1520_shaywitz/sn1520_shaywitz_stack4d_S707_020.hdr
sn1567_shaywitz/sn1567_shaywitz_stack4d_S707_020.hdr
sn1575_shaywitz/sn1575_shaywitz_stack4d_S707_020.hdr
sn1576_shaywitz/sn1576_shaywitz_stack4d_S707_020.hdr
sn1590_shaywitz/sn1590_shaywitz_stack4d_S707_020.hdr
sn1595_shaywitz/sn1595_shaywitz_stack4d_S707_020.hdr
sn1604_shaywitz/sn1604_shaywitz_stack4d_S707_020.hdr
sn1622_shaywitz/sn1622_shaywitz_stack4d_S707_020.hdr
sn1623_shaywitz/sn1623_shaywitz_stack4d_S707_020.hdr
sn1624_shaywitz/sn1624_shaywitz_stack4d_S707_020.hdr
sn1638_shaywitz/sn1638_shaywitz_stack4d_S707_020.hdr
sn1646_shaywitz/sn1646_shaywitz_stack4d_S707_020.hdr
sn1651_shaywitz/sn1651_shaywitz_stack4d_S707_020.hdr
sn1656_shaywitz/sn1656_shaywitz_stack4d_S707_020.hdr
sn1658_shaywitz/sn1658_shaywitz_stack4d_S707_020.hdr
sn1687_shaywitz/sn1687_shaywitz_stack4d_S707_020.hdr
sn1761_shaywitz/sn1761_shaywitz_stack4d_S707_020.hdr
sn1772_shaywitz/sn1772_shaywitz_stack4d_S707_020.hdr
sn1829_shaywitz/sn1829_shaywitz_stack4d_S707_020.hdr
sn1940_shaywitz/sn1940_shaywitz_stack4d_S707_020.hdr
sn2036_shaywitz/sn2036_shaywitz_stack4d_S707_020.hdr
sn2435_shaywitz/sn2435_shaywitz_stack4d_S707_020.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