# Example Batch File
# The following variables can be defined
# inputlist(1) .. inputlist(9) :  lists of inputs
# outputsuffix : list of outputsuffices
# cmdline : the command line beginning with the algorithm
# logsuffix : the suffix of the log file for each command


set inputlist(1) {
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr 
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr 
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr 
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr   
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr 
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr  
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr  
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr    
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
Time1_mnc/nu_XXXAB_crop_LPS.nii.hdr
}

set inputlist(2) {
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr  
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr 
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr 
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr  
Time2mnc/nu_XXXAB_crop_LPS._nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr 
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
Time2mnc/nu_XXXAB_crop_LPS.nii.hdr
}


#Use the *ignore* flag to skip an optional input, i.e. in this case -inp3 will not be used
set inputlist(3) {
    *ignore*
}

set inputlist(4) {
    *ignore*
}

set inputlist(5) {
   *ignore*
}

set outputsuffix {
    map_9.grd
}

set logsuffix "results"

set cmdline "bis_nonlinearintensityregister.tcl --initialmode rigid --spacing 9 --smoothness 0 --numberoflevels 3 --resolution 1.2 --useinitial 0 --reslimage Resliced --metric NMI --useweightimage 0 --iterations 15 --resolutionrate 2 --autonormalize 1 --optimization default --numberofbins 64 --spacingrate 2.0 --extralevels 0 --windowsize 1.0 --numberofsteps 1 --stepsize 1.0 --usegpu 0 --threadmode 3 --directstorage 1"