Let and be corresponding template and target landmarks respectively. Find the rotation, , translation , and scale which minimize

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)

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

Typical Usage and Parameters:

lddmm-similitude [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. -a --all-info: print data provenance info
   2. -x --all-info-xml: print data provenance info in an xml format
   3. -v --version: print program version 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 ]

   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: Monday, 08-Jan-2007 10:27:13 EST