Batch registration

In order to run registration in batch, you must write a script. Because I am a perl guy, this example is written in perl.:

#!/usr/bin/perl
# This example shows how to register a group of images in batch

# This is a template for the command file.  Each registration will
# substitute the strings FIXED, MOVING, WARPED, and VF.
$template = <<EODATA
[GLOBAL]
fixed=FIXED
moving=MOVING
img_out=WARPED
vf_out=VF
[STAGE]
xform=bspline
res=1 1 1
grid_spac=4 4 4
regularization_lambda=0.1
max_iterations=11
[STAGE]
max_iterations=11
EODATA
  ;

# Create an array with the filenames of the moving and fixed images
# In this case, there is a single moving image (00001.nrrd) and a bunch
# of fixed images (00001.nrrd through 00500.nrrd)
@moving_images = ( "00001.nrrd" );
@fixed_images = <000*.nrrd>;

# Loop through both lists
for $f (@fixed_images) {
  for $m (@moving_images) {

    # Get the "number" portion of the filenames
    $f =~ m/([0-9]*)/;
    $f_image_no = $1;
    $m =~ m/([0-9]*)/;
    $m_image_no = $1;

    # Create filenames for the output files
    $warped = "${f_image_no}_${m_image_no}.nrrd";
    $vf = "${f_image_no}_${m_image_no}_vf.nrrd";

    # Substitute the image filenames into the template
    $t = $template;
    $t =~ s/FIXED/$f/;
    $t =~ s/MOVING/$m/;
    $t =~ s/WARPED/$warped/;
    $t =~ s/VF/$vf/;

    # Write the command file
    open FH, ">", "parameters.txt";
    print FH $t;
    close FH;

    # Run plastimatch on the command file
    $cmd = "plastimatch register ${pfn}";
    system ($cmd);
  }
}