#Example Setup File
# all lines beginning with # are ignored 
#
#
#
# List all subjects here
#
set imglist {
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
sn698_shaywitz/sn698_3D_stripped.hdr
sn703_shaywitz/sn703_3D_stripped.hdr
sn744_shaywitz/sn744_3D_stripped.hdr
sn793_shaywitz/sn793_3D_stripped.hdr
sn925_shaywitz/sn925_3D_stripped.hdr
sn939_shaywitz/sn939_3D_stripped.hdr
sn958_shaywitz/sn958_3D_stripped.hdr
}
#
#
#
# Put reference brain here
#
set refimg  /data1/temp_space/lacadie/ref3d/XeniosBrain/Reslice_axial.hdr

#set refimg /data1/temp_space/lacadie/ref3d/ColinBrain/colin_1p5mm_strip.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
#
#
# Tweak parameters
# filetype = 1 includes directory name in output filename 0 does not
# order = normal does normal registration i.e. map image to reference
# order = strip  maps reference to image (for brainstripping)
set resolution 1.5
set spacing   20.0
set iterations 15
set order        "normal"
set filenametype 0
set smoothness   0.005