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Software at CIS : lddmm-similitude and lddmm-rigid

Algorithm

Let $x_1, ... , x_N$ and $y_1, ... , y_N$ be corresponding template and target landmarks respectively. Find the rotation, $R$, translation $t$, and (for lddmm-similitude) scale $s$ which minimize

\begin{displaymath} \sum_{i=1}^N \vert\vert y_i-sRx_i-t\vert\vert^2. \end{displaymath}

For lddmm-rigid, scale $s$ is fixed at 1.0.

Reference

S. Umeyama, "Least-Squares Estimation of Transformation Parameters Between Two Point Patterns".IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol 12, NO 4, April 1991. (pdf)

lddmm-similitude matching is a program to determine the similarity between two landmark data sets based on rotation, translation, and scale. The program will write the rotation, translation and scale to standard out and create a file representing the transformed template.

lddmm-rigid matching is a program to determine the similarity between two landmark data sets based on rotation and translation. The program will write the rotation and translation to standard out and create a file representing the transformed template.

Typical Usage and Parameters:

lddmm-similitude || lddmm-rigid [OPTIONS] x_file y_file tx_file norm_constant [Rts_file]


The following are the command line options.

  1. x_file: the template landmark file
  2. y_file: the target landmark file
  3. tx_file: the output file containing the transformed template. Use /dev/null if this is not required.
  4. norm_constant: always use 1.0
  5. Rts_file: omit this option
  6. Options:
  1. -r --allowReflection: allow a transform that includes a reflection
  2. -a --all-info: print data provenance info
  3. -x --all-info-xml: print data provenance info in an xml format
  4. -v --version: print program version information
  5. -h --help: print program usage information
Landmark File Format:

The format for a 2-D landmark file is as follows: 
 N x 2
 [ x_0 y_0
   x_1 y_1
   .
   .
   x_N y_N ]

And for a 3-D file: 

 N x 3
 [ x_0 y_0 z_0
   x_1 y_1 z_1
   .
   .
   x_N y_N z_N ]

Output File Format:

The program will format the output file based on the extension of the output file:

  • bz - blitz++ (or runSim) format, described above.
  • lmk - BrainWorks format.
  • fcsv - Slicer 3D fiducial format.
Scripting:
Here is an example Perl script that computes the similarity for every pair of landmark sets in start_folder and writes the output line by line to a text file for later analysis. This can easily be adapted to do different comparisons (ex. left & right data separately) by calling the function do_sims on a number of different lists: 
#!/usr/bin/perl
$program = "lddmm-similitude";
$start_folder = "/cis/project/botteron/hippocampus/Converted_Lmk";

@inlist= `ls -1 $start_folder/*.lmk`;
$outfile = "/cis/project/botteron/hippocampus/left_scale_list.txt";

&do_sims ($infile, \@outlist);

sub do_sims {
  my $outfile = shift;
  my $list_ref=shift;
  my @list = @$list_ref;
  print "$outfile\n";
  print "List size: $#list\n";

  for($i=0; $i<=$#list; $i++) {
    chomp $list[$i];
    $list[$i] =~ /^.+\/(.+)/;
    $shortlist[$i] = $1;
  }
  open OUT, "> $outfile";
  for($i=0; $i<=$#list; $i++) {
    for($j=$i+1; $j<=$#list; $j++) {
      $sim = `$program $list[$i] $list[$j] /dev/null 1.0 | cut -f3 -d\\ `;
      print OUT "$shortlist[$i]:$shortlist[$j]:$sim";
    }
    print "Finished $shortlist[$i]\n";
  }
  close OUT;
}

Software developed with support from National Institutes of Health NCRR grant P41 RR15241.

Last Modified: Friday, 15th April, 2011 @ 11:12am

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