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ana2mnc_xfm_reduce.pl
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#! /usr/bin/env perl
#
# Andrew Janke - a.janke@gmail.com
# Center for Magnetic Resonance
# The University of Queensland
#
# MINC is a free file format from the MNI: www.bic.mni.mcgill.ca
# ANALYZE is a commercial file format from the mayo clinic: www.mayo.edu/bir
# SPM is a free fMRI toolkit using a hybrid ANALYZE format: www.fil.ion.bpmf.ac.uk/spm
#
# Inspired by Peter Neelins' (neelin@bic.mni.mcgill.ca) ana2mnc for ANALYZE 4.x.
# Since then it has grown into a veritable swiss-army chainsaw of
# SPM, ANALYZE 7.5 and MINC conversion.
#
# The reading and transformation of SPM .mat files to minc .xfm files is
# Still somewhat experimental: The following is from spm_realign.m
# x1 = M(1,1)*x0 + M(1,2)*y0 + M(1,3)*z0 + M(1,4)
# y1 = M(2,1)*x0 + M(2,2)*y0 + M(2,3)*z0 + M(2,4)
# z1 = M(3,1)*x0 + M(3,2)*y0 + M(3,3)*z0 + M(3,4)
# This is equivalent to the MINC version (if you dig enough in the MINC
# distribution you will find a file volume_io/Geometry/transforms.c)
# in the function: homogenous_transform_point
# The actual matrix decomposing is analagous to Louis Collins's
# extract_parameters_from_matrix in minctracc/Numerical/make_rots.c
# in mni_autoreg package
#
# It can be invoked as:
# ana2mnc - convert ANALYZE 7.5 to MINC
# mnc2ana - convert MINC to ANALYZE 7.5
# ana_show - Show the contents of an ANALYZE 7.5 header
# ana_write - write an ANALYZE header (requires gobs of additional CL arguments)
#
# Wed Oct 18 09:29:44 EST 2000 - updated to Analyze 7.5 format
# Thu Oct 19 16:57:30 EST 2000 - Added support for writing out ANALYZE 7.5 headers
# Wed Oct 25 10:29:54 EST 2000 - Added mnc2ana, ana_show and ana_write functionality
# Tue Nov 28 15:58:57 EST 2000 - Completed transformation decomposition added xfm_reduce
require 5.0;
use strict;
use warnings "all";
use Math::Trig;
use Math::MatrixReal;
use MNI::Startup qw(nocputimes);
use MNI::MincUtilities qw(:range :geometry);
use Getopt::Tabular;
my($clobber) = '';
my($verbose) = 0;
my($spm) = 0;
my($args_h) = create_analyze_header();
my(@opt_table) = (
["-verbose", "boolean", 0, \$verbose, "Be Verbose"],
["-clobber", "const", "-clobber", \$clobber, "clobber existing files"],
["-spm", "boolean", 0, \$spm, "Read in the SPM .mat as well"],
$h->{data_type} = 0;
$h->{db_name} = '';
$h->{regular} = 'r';
$h->{hkey_un0} = 0;
$h->{dim} = [0,0,0,0,0,0,0,0];
$h->{vox_units} = '';
$h->{cal_units} = '';
$h->{unused1} = 0;
$h->{datatype} = 0;
$h->{bitpix} = 0;
$h->{dim_un0} = 0;
$h->{pixdim} = [0,0,0,0,0,0,0,0];
$h->{vox_offset} = 0;
$h->{scale_factor} = 1.0;
$h->{funused1} = 0;
$h->{funused2} = 0;
$h->{cal_max} = 0;
$h->{cal_min} = 0;
$h->{compressed} = 0;
$h->{verified} = 0;
$h->{glmax} = 0;
$h->{glmin} = 0;
$h->{descrip} = '';
$h->{aux_file} = '';
$h->{orient} = 0;
$h->{originator} = [0,0,0,0,0];
$h->{generated} = '';
$h->{scannum} = '';
$h->{patient_id} = '';
$h->{exp_date} = '';
$h->{exp_time} = '';
$h->{hist_un0} = '';
$h->{views} = 0;
$h->{vols_added} = 0;
$h->{start_field} = 0;
$h->{field_skip} = 0;
$h->{omax} = 0;
$h->{omin} = 0;
$h->{smax} = 0;
$h->{smin} = 0;
}
);
chomp(my($prog) = `basename $0`);
my $files; my $nfiles;
if ($prog eq "ana2mnc"){ $files = "<in.hdr> <out.mnc>"; $nfiles = 2; }
elsif ($prog eq "mnc2ana"){ $files = "<in.mnc> <out.hdr>"; $nfiles = 2; }
elsif ($prog eq "ana_show"){ $files = "<in.hdr>"; $nfiles = 1; }
elsif ($prog eq "ana_write"){ $files = "<out.hdr>"; $nfiles = 1; }
elsif ($prog eq "spm_show"){ $files = "<in.mat>"; $nfiles = 1; }
elsif ($prog eq "spm_conv"){ $files = "<in.mat>"; $nfiles = 1; }
elsif ($prog eq "xfm_reduce"){ $files = "<in.xfm>"; $nfiles = 1; }
my($Usage) = "Usage: $prog [options] $files\n".
"$prog -help to list options\n";
my($Help) = <<HELP;
This script can be invoked as:
ana2mnc Convert a ANALYZE 7.5 .hdr .img couple to a MINC file
mnc2ana Convert a MINC file to a ANALYZE 7.5 .hdr .img couple
ana_show Show the contents of a ANALYZE 7.5 .hdr file
ana_write Write a ANALYZE .hdr file from input arguments
spm_show Show the contents of a SPM normalization .mat file
spm_conv Convert a SPM normalization .mat to a .xfm file
xfm_reduce Reduce a MNI .xfm file to it least form
HELP
# Check arguments
&Getopt::Tabular::SetHelp ($Help, $Usage);
&GetOptions (\@opt_table, \@ARGV) || exit 1;
if ($#ARGV < $nfiles - 1){ die $Usage; }
my($mncfile, $anafile, $xfmfile);
if ($prog eq "ana2mnc"){
($anafile, $mncfile) = @ARGV[0..1];
$anafile =~ s/\....$//;
if (!-e "$anafile.hdr" || !-e "$anafile.img"){
die "$prog: Couldn't find $anafile.hdr and $anafile.img\n";
}
if (-e $mncfile && ($clobber ne "-clobber")){
die "$prog: $mncfile exists! use -clobber to overwrite\n";
}
# Read in the header file
my($h) = read_analyze_header("$anafile.hdr");
if ($verbose){ print STDOUT dump_analyze_header($h); }
write_minc($h, $mncfile, "$anafile.img");
}
elsif ($prog eq "mnc2ana"){
($mncfile, $anafile) = @ARGV[0..1];
$anafile =~ s/\....$//;
if (!-e $mncfile){
die "$prog: Couldn't find $mncfile\n";
}
if ((-e "$anafile.hdr" || -e "$anafile.img") && ($clobber ne "-clobber")){
die "$prog: $anafile.hdr or $anafile.img exist! use -clobber to overwrite\n";
}
my($h) = read_minc($mncfile);
if ($verbose){ print STDOUT dump_analyze_header($h); }
write_analyze_header($h, "$anafile.hdr");
# Set up mincextract command
my $args = "mincextract -normalize -positive_direction -filetype ";
$args .= ($h->{bitpix} == 8) ? '-unsigned ' : '-signed ';
$args .= "$mncfile > $anafile.img\n";
if ($verbose){ print STDOUT $args; }
system($args) == 0 or die "Died during mincextract command\n";
}
elsif ($prog eq "ana_show"){
$anafile = $ARGV[0];
$anafile =~ s/\....$//;
if (!-e "$anafile.hdr"){ die "$prog: Couldn't find $anafile.hdr\n"; }
print STDOUT dump_analyze_header(read_analyze_header("$anafile.hdr"));
}
elsif ($prog eq "ana_write"){
$anafile = $ARGV[0];
$anafile =~ s/\....$//;
if (-e "$anafile.hdr" && ($clobber ne "-clobber")){
die "$prog: $anafile.hdr exists! use -clobber to overwrite\n";
}
my($h) = create_analyze_header();
write_analyze_header($h, "$anafile.hdr");
}
elsif ($prog eq "spm_show"){
$anafile = $ARGV[0];
$anafile =~ s/\....$//;
if (!-e "$anafile.mat"){ die "$prog: Couldn't find $anafile.mat\n"; }
print STDOUT `mat1dump $anafile.mat`;
}
elsif ($prog eq "spm_conv"){
$anafile = $ARGV[0];
$anafile =~ s/\....$//;
chomp(my $date = `date`);
my($M, @Trans, @Scale, @Shear, @Rotn);
if (!-e "$anafile.mat"){ die "$prog: Couldn't find $anafile.mat\n"; }
# perl line noise to read in a text file Matrix into MatrixReal
my @matdump = `mat1dump $anafile.mat`;
$M = Math::MatrixReal->new_from_string("[ " . join(" ]\n[ ", @matdump[1..4]) . " ]\n");
if ($verbose){ print STDERR "M:\n$M"; }
decompose_transformation_matrix($M, \@Trans, \@Scale, \@Shear, \@Rotn);
print_transformation_matrix($M, "M");
my (@resliceR, $sign);
my $c = 0;
foreach (@Rotn){
$resliceR[$c] = 0;
$sign = $_/abs($_);
if (abs($_) > pi()){ die "$prog: Bugger! this angle is too big!: $_\n"; }
if (abs($_) > pi()/2){ # if 90 deg
$Rotn[$c] -= $sign * pi()/2;
$resliceR[$c] += $sign * pi()/2;
}
if (abs($_) > pi()/4){ # if 45 deg reverse the rotation (subtract 90deg).
$Rotn[$c] -= $sign * pi()/2;
$resliceR[$c] += $sign * pi()/2;
}
$c ++;
}
my $RESLICE = create_transformation_matrix(undef, undef, undef, \@resliceR);
print_transformation_matrix($RESLICE, "RESLICE");
my $MINCxfm = create_transformation_matrix(\@Trans, \@Scale, \@Shear, \@Rotn);
$MINCxfm = $M * $RESLICE->decompose_LR()->invert_LR();
print_transformation_matrix($MINCxfm, "MINCxfm");
print_transformation_matrix($MINCxfm * $RESLICE, "CHECK");
open(SPM_XFM, ">$anafile.spm_xfm");
print SPM_XFM "SPM Transform File\n".
"%$date>>> Created by $prog from $anafile.mat\n\n".
"@matdump[1..3]";
close(SPM_XFM);
}
elsif ($prog eq "xfm_reduce"){
$xfmfile = $ARGV[0];
my($Mtext, $M, @Trans, @Scale, @Shear, @Rotn);
if (!-e "$xfmfile"){ die "$prog: Couldn't find $xfmfile\n"; }
# perl line noise to read in a text file Matrix into MatrixReal
my @MNIdump = `cat $xfmfile`;
my $line;
do{ $line = shift(@MNIdump) or die "$prog: Couldn't find a MNI Transform in: $xfmfile\n";}
until $line =~ m/Linear_Transform/;
foreach (@MNIdump[0..2]){
chomp;
s/\;//;
$Mtext .= "[ $_ ]\n";
}
$Mtext .= "[ 0 0 0 1 ]\n";
$M = Math::MatrixReal->new_from_string($Mtext);
decompose_transformation_matrix($M, \@Trans, \@Scale, \@Shear, \@Rotn);
my $c = 0;
foreach (@Rotn){
$Rotn[$c] = rad2deg($_);
$c ++;
}
printf("Translation: %10.5f %10.5f %10.5f\n", @Trans);
printf("Rotation: %10.5f %10.5f %10.5f\n", @Rotn);
printf("Scale: %10.5f %10.5f %10.5f\n", @Scale);
printf("Shear: %10.5f %10.5f %10.5f\n", @Shear);
}
# Subroutines #######################################################
# Unpack a value from a string (passed by reference)
sub destruct{
my($stringref, $offset, $type) = @_;
return unpack("x$offset $type", $$stringref);
}
# Read an analyze 7.5 header file and return a hash
sub read_analyze_header{
open(HDR, $_[0]) or die "Error opening file: $_[0]\n";
read(HDR, my($hdr_s), 40);
read(HDR, my($dim_s), 108);
read(HDR, my($his_s), 200);
close(HDR);
my($h) = {};
$h->{sizeof_hdr} = destruct(\$hdr_s, 0,'i' ); # 4 - the byte size of the header file
$h->{data_type} = destruct(\$hdr_s, 4,'a10'); # 10 -
$h->{db_name} = destruct(\$hdr_s, 14,'a18'); # 18 -
$h->{extents} = destruct(\$hdr_s, 32,'i' ); # 4 - should be 16384
$h->{session_error} = destruct(\$hdr_s, 36,'s' ); # 2 -
$h->{regular} = destruct(\$hdr_s, 38,'a' ); # 1 - 'r' indicates volumes are the same size
$h->{hkey_un0} = destruct(\$hdr_s, 39,'c' ); # 1 -
# 40 bytes
$h->{dim} =[destruct(\$dim_s, 0,'s8' )]; # 16 - array of the image dimensions
# dim[0] # of dimensions; usually 4
# dim[1] X dim - pixels in an image row
# dim[2] Y dim - pixel rows in slice
# dim[3] Z dim - slices in a volume
# dim[4] Time dim - volumes in database
$h->{vox_units} = destruct(\$dim_s, 16,'a4' ); # 4 - spatial units of measure for a voxel
$h->{cal_units} = destruct(\$dim_s, 20,'a8' ); # 8 - name of the calibration unit
$h->{unused1} = destruct(\$dim_s, 28,'s' ); # 2
$h->{datatype} = destruct(\$dim_s, 30,'s' ); # 2 - datatype for this image set
$h->{bitpix} = destruct(\$dim_s, 32,'s' ); # 2 - # of bits per voxel 1, 8, 16, 32, or 64.
$h->{dim_un0} = destruct(\$dim_s, 34,'s' ); # 2 -
$h->{pixdim} =[destruct(\$dim_s, 36,'f8' )]; # 32 - pixdim[] specifies the voxel dimensions:
# pixdim[1] - voxel width
# pixdim[2] - voxel height
# pixdim[3] - interslice distance
# ..etc
$h->{vox_offset} = destruct(\$dim_s, 68,'f' ); # 4 - byte offset in .img at which voxels start.
# This value can be negative to specify
# that the absolute value is applied for
# every image
$h->{scale_factor} = destruct(\$dim_s, 72,'f' ); # 4 = funused1; scale factor used by SPM
$h->{funused1} = destruct(\$dim_s, 76,'f' ); # 4
$h->{funused2} = destruct(\$dim_s, 80,'f' ); # 4
$h->{cal_max} = destruct(\$dim_s, 84,'f' ); # 4 - calibrated max & min:
$h->{cal_min} = destruct(\$dim_s, 88,'f' ); # 4 www.mailbase.ac.uk/lists/spm/2000-09/0099.html
$h->{compressed} = destruct(\$dim_s, 92,'f' ); # 4
$h->{verified} = destruct(\$dim_s, 96,'f' ); # 4
$h->{glmax} = destruct(\$dim_s,100,'i' ); # 4 - global max | pixel values
$h->{glmin} = destruct(\$dim_s,104,'i' ); # 4 - global min | (entire database)
#108 bytes
$h->{descrip} = destruct(\$his_s, 0,'a80'); # 80
$h->{aux_file} = destruct(\$his_s, 80,'a24'); # 24
$h->{orient} = destruct(\$his_s,104,'c' ); # 1 - slice orientation | disregarded
# 0 - transverse unflipped | by SPM
# 1 - coronal unflipped | instead a
# 2 - sagittal unflipped | .mat file is
# 3 - transverse flipped | written out
# 4 - coronal flipped | with this
# 5 - sagittal flipped | information
$h->{originator} =[destruct(\$his_s,105,'s5' )]; # 10 - origin
# originator[0] x-origin | non standard
# originator[1] y-origin | SPM use only
# originator[2] z-origin |
$h->{generated} = destruct(\$his_s,115,'a10'); # 10
$h->{scannum} = destruct(\$his_s,125,'a10'); # 10
$h->{patient_id} = destruct(\$his_s,135,'a10'); # 10
$h->{exp_date} = destruct(\$his_s,145,'a10'); # 10
$h->{exp_time} = destruct(\$his_s,155,'a10'); # 10
$h->{hist_un0} = destruct(\$his_s,165,'a3' ); # 3
$h->{views} = destruct(\$his_s,168,'i' ); # 4
$h->{vols_added} = destruct(\$his_s,172,'i' ); # 4
$h->{start_field} = destruct(\$his_s,176,'i' ); # 4
$h->{field_skip} = destruct(\$his_s,180,'i' ); # 4
$h->{omax} = destruct(\$his_s,184,'i' ); # 4
$h->{omin} = destruct(\$his_s,188,'i' ); # 4
$h->{smax} = destruct(\$his_s,192,'i' ); # 4
$h->{smin} = destruct(\$his_s,196,'i' ); # 4
#200 bytes
return $h;
}
# return a ASCII dump of an ANALYZE 7.5 header
sub dump_analyze_header{
my($h) = shift;
return
"HDR:\n".
" sizeof_hdr <$h->{sizeof_hdr}>\n".
" data_type <$h->{data_type}>\n".
" db_name <$h->{db_name}>\n".
" extents <$h->{extents}>\n".
" session_error <$h->{session_error}>\n".
" regular <$h->{regular}>\n".
" hkey_un0 <$h->{hkey_un0}>\n".
"DIMENSION:\n".
" dim: <" . join(' ', @{$h->{dim}}) . ">\n".
" vox_units <$h->{vox_units}>\n".
" cal_units <$h->{cal_units}>\n".
" unused1 <$h->{unused1}>\n".
" datatype <$h->{datatype}>\n".
" bitpix <$h->{bitpix}>\n".
" dim_un0 <$h->{dim_un0}>\n".
" pixdim <" . join(' ', @{$h->{pixdim}}) . ">\n".
" vox_offset <$h->{vox_offset}>\n".
" scale_factor <$h->{scale_factor}>\n".
" funused1 <$h->{funused1}>\n".
" funused2 <$h->{funused2}>\n".
" cal_max <$h->{cal_max}>\n".
" cal_min <$h->{cal_min}>\n".
" compressed <$h->{compressed}>\n".
" verified <$h->{verified}>\n".
" glmax <$h->{glmax}>\n".
" glmin <$h->{glmin}>\n".
"HISTORY:\n".
" descrip <$h->{descrip}>\n".
" aux_file <$h->{aux_file}>\n".
" orient <$h->{orient}>\n".
" originator <" . join(' ', @{$h->{originator}}) . ">\n".
" generated <$h->{generated}>\n".
" scannum <$h->{scannum}>\n".
" patient_id <$h->{patient_id}>\n".
" exp_date <$h->{exp_date}>\n".
" exp_time <$h->{exp_time}>\n".
" hist_un0 <$h->{hist_un0}>\n".
" views <$h->{views}>\n".
" vols_added <$h->{vols_added}>\n".
" start_field <$h->{start_field}>\n".
" field_skip <$h->{field_skip}>\n".
" omax <$h->{omax}>\n".
" omin <$h->{omin}>\n".
" smax <$h->{smax}>\n".
" smin <$h->{smin}>\n";
}
# Write an ANALYZE 7.5 header to a file
sub write_analyze_header{
my($h, $hdrfile) = @_;
my $hdr_s = pack("i", $h->{sizeof_hdr} );
$hdr_s .= pack("a10", $h->{data_type} );
$hdr_s .= pack("a18", $h->{db_name} );
$hdr_s .= pack("i", $h->{extents} );
$hdr_s .= pack("s", $h->{session_error} );
$hdr_s .= pack("a", $h->{regular} );
$hdr_s .= pack("c", $h->{hkey_un0} );
my $dim_s = pack("s8", @{$h->{dim}}[0..7] );
$dim_s .= pack("a4", $h->{vox_units} );
$dim_s .= pack("a8", $h->{cal_units} );
$dim_s .= pack("s", $h->{unused1} );
$dim_s .= pack("s", $h->{datatype} );
$dim_s .= pack("s", $h->{bitpix} );
$dim_s .= pack("s", $h->{dim_un0} );
$dim_s .= pack("f8", @{$h->{pixdim}}[0..7] );
$dim_s .= pack("f", $h->{vox_offset} );
$dim_s .= pack("f", $h->{scale_factor} );
$dim_s .= pack("f", $h->{funused1} );
$dim_s .= pack("f", $h->{funused2} );
$dim_s .= pack("f", $h->{cal_max} );
$dim_s .= pack("f", $h->{cal_min} );
$dim_s .= pack("f", $h->{compressed} );
$dim_s .= pack("f", $h->{verified} );
$dim_s .= pack("i", $h->{glmax} );
$dim_s .= pack("i", $h->{glmin} );
my $his_s = pack("a80",$h->{descrip} );
$his_s .= pack("a24", $h->{aux_file} );
$his_s .= pack("c", $h->{orient} );
$his_s .= pack("s5", @{$h->{originator}}[0..4] );
$his_s .= pack("a10", $h->{generated} );
$his_s .= pack("a10", $h->{scannum} );
$his_s .= pack("a10", $h->{patient_id} );
$his_s .= pack("a10", $h->{exp_date} );
$his_s .= pack("a10", $h->{exp_time} );
$his_s .= pack("a3", $h->{hist_un0} );
$his_s .= pack("i", $h->{views} );
$his_s .= pack("i", $h->{vols_added} );
$his_s .= pack("i", $h->{start_field} );
$his_s .= pack("i", $h->{field_skip} );
$his_s .= pack("i", $h->{omax} );
$his_s .= pack("i", $h->{omin} );
$his_s .= pack("i", $h->{smax} );
$his_s .= pack("i", $h->{smin} );
open(HDR, ">$hdrfile") or die "Error opening file: $hdrfile\n";
syswrite(HDR, $hdr_s, 40);
syswrite(HDR, $dim_s, 108);
syswrite(HDR, $his_s, 200);
close(HDR);
}
# Create and return an ANALYZE 7.5 as a hash
sub create_analyze_header{
my($h) = {};
$h->{sizeof_hdr} = 348; $h->{data_type} = 0;
$h->{db_name} = ''; $h->{extents} = 16384;
$h->{session_error} = 0; $h->{regular} = 'r';
$h->{hkey_un0} = 0;
$h->{dim} = [0,0,0,0,0,0,0,0];
$h->{vox_units} = ''; $h->{cal_units} = '';
$h->{unused1} = 0; $h->{datatype} = 0;
$h->{bitpix} = 0; $h->{dim_un0} = 0;
$h->{pixdim} = [0,0,0,0,0,0,0,0];
$h->{vox_offset} = 0; $h->{scale_factor} = 1.0;
$h->{funused1} = 0; $h->{funused2} = 0;
$h->{cal_max} = 0; $h->{cal_min} = 0;
$h->{compressed} = 0; $h->{verified} = 0;
$h->{glmax} = 0; $h->{glmin} = 0;
$h->{descrip} = ''; $h->{aux_file} = '';
$h->{orient} = 0; $h->{originator} = [0,0,0,0,0];
$h->{generated} = ''; $h->{scannum} = '';
$h->{patient_id} = ''; $h->{exp_date} = '';
$h->{exp_time} = ''; $h->{hist_un0} = '';
$h->{views} = 0; $h->{vols_added} = 0;
$h->{start_field} = 0; $h->{field_skip} = 0;
$h->{omax} = 0; $h->{omin} = 0;
$h->{smax} = 0; $h->{smin} = 0;
return $h;
}
# Write out a MINC file based upon a given ANALYZE 7.5 header and a raw data file
sub write_minc{
my($h, $mncfile, $imgfile) = @_;
my(%dtypes) = (
0 => ['-short', '-unsigned'],
2 => ['-byte', '-unsigned'],
4 => ['-short', '-signed'],
8 => ['-long', '-signed'],
16 => ['-float'],
64 => ['-double'],
128 => ['-byte', '-unsigned', '-vector', '3']
);
# Check the data type
if (!defined($dtypes{$h->{datatype}})){ die "Unknown data type: $h->{datatype}\n"; }
# Gethistory string
chomp(my($history) = `date`);
$history .= '>>>> ' . join(' ', $prog, @ARGV);
# Get step info
my(@world_order);
if (($h->{orient} == 0) || ($h->{orient} == 3)){ # Transverse
$h->{orientation} = '-transverse';
@world_order = (1, 2, 3);
}
elsif (($h->{orient} == 1) || ($h->{orient} == 4)){ # Coronal
$h->{orientation} = '-coronal';
@world_order = (1, 3, 2);
}
elsif (($h->{orient} == 2) || ($h->{orient} == 5)){ # Sagittal
$h->{orientation} = '-sagittal';
@world_order = (3, 1, 2);
}
else{ # Unknown
warn "Unknown data orientation: assuming transverse\n";
$h->{orientation} = '-transverse';
@world_order = (1, 2, 3);
}
my(@steps) = @{$h->{pixdim}}[@world_order];
# set up the steps in mm co-ordinates (as opposed to ANALYZE voxel co-ordinates)
my($c) = 0;
foreach (@steps){
print "$c: $_ @{$h->{originator}}[$c]\n";
@{$h->{originator}}[$c] = (@{$h->{originator}}[$c])*$_;
print "$c: $_ @{$h->{originator}}[$c]\n";
$c ++;
}
# Set up rawtominc command
my($args) = "rawtominc $clobber @{$dtypes{$h->{datatype}}} ".
"-range $h->{glmin} $h->{glmax} ";
$args .= ($h->{cal_min} < $h->{cal_max})
? "-real_range $h->{cal_min} $h->{cal_max} "
: "-scan_range ";
$args .= "$h->{orientation} ".
"-xstep $steps[0] -ystep $steps[1] -zstep $steps[2] ".
"-origin @{$h->{originator}}[0, 1, 2] ".
"-sattribute :history='$history' ".
"-input $imgfile $mncfile ";
$args .= (@{$h->{dim}}[4] > 1) ? "@{$h->{dim}}[4] " : '';
$args .= "@{$h->{dim}}[3, 2, 1]\n";
# Check for compressed input
if (!-e $imgfile && -e "$imgfile.gz"){
system("gunzip $imgfile.gz\n") == 0 or die "Died during gunzip\n";
}
if ($verbose){ print STDOUT $args; }
system($args) == 0 or die "Died during rawtominc system command\n";
}
# Read a minc file header and return an appropriate ANALYZE 7.5 header
sub read_minc{
my($mncfile) = shift;
my(@start, @step, @length, @dir_cosines, @dims, $permutation);
my($h) = create_analyze_header();
# ($h->{cal_min}, $h->{cal_max}) = volume_minmax($mncfile);
$h->{glmin} = 0;
$h->{glmax} = 65535;
volume_params($mncfile, \@start, \@step, \@length, \@dir_cosines, \@dims);
$permutation = (&get_dimension_order($mncfile))[1];
my $c = 0;
$h->{dim}[$c] = $h->{pixdim}[$c] = $#{$permutation} + 2;
foreach (@{$permutation}){
$h->{dim}[$c+1] = $length[$c];
$h->{pixdim}[$c+1] = abs($step[$c]);
$c ++;
}
# contains: 0 corresponding ANALYZE datatype
# 1 corresponding ANALYZE bitpix
# 2 min
# 3 max
my(%dtypes) = ( 'byte' => [ 2, 8, 0, 256], # unsigned
'short' => [ 4, 16, -32767, 32767], # signed
'long' => [ 8, 32, ], # signed
'float' => [ 16, 32, ],
'double' => [ 64, 64, ],
'vector' => [128, 24, ],
);
chomp(my $dt = `mincinfo -vartype image $mncfile`);
$h->{datatype} = $dtypes{$dt}[0];
$h->{bitpix} = $dtypes{$dt}[1];
return $h;
}
# Takes a 4x4 transformation matrix $M (using the Math:MatrixReal module)
# Returns the translation, scale, shear and rotations encoded in the input
# matrix.
#
# Andrew Janke - a.janke@gmail.com
# Losely based on Louis Collins' make_rots.c from the mni_autoreg package
# With substantial help from Mark Griffin - mark.griffin@cmr.uq.edu.au
sub decompose_transformation_matrix{
my($M, $Trans, $Scale, $Shear, $Rotn) = @_;
my ($Sx, $Sy, $Sz, $SHa, $SHb, $SHc, $Rx, $Ry, $Rz);
# TRANSLATIONS - [M] = [T][S][SH][R]
# As of yet I am assuming the center of rotation is (0,0,0) as
# I am not exactly sure as to what SPM does here.
@$Trans[0] = $M->element(1, 4);
@$Trans[1] = $M->element(2, 4);
@$Trans[2] = $M->element(3, 4);
my $T = $M->shadow(); $T->one(); # Create and zero the Translation Matrix
$T->assign(1, 4, @$Trans[0]);
$T->assign(2, 4, @$Trans[1]);
$T->assign(3, 4, @$Trans[2]);
# SCALES - [M] = inv[T][T][S][SH][R] = [S][SH][R]
# Here we use an identical method to Louis Collins's in mni_autoreg
# Namely multiply a unit vector in each direction and measure the length
# after the transformation.
$M = $T->decompose_LR()->invert_LR() * $M;
my $SSHRinv = $M->decompose_LR()->invert_LR();
my $Unit = Math::MatrixReal->new(4, 1);
$Unit->zero(); $Unit->assign(1, 1, 1); $Sx = ($SSHRinv * $Unit)->length();
$Unit->zero(); $Unit->assign(2, 1, 1); $Sy = ($SSHRinv * $Unit)->length();
$Unit->zero(); $Unit->assign(3, 1, 1); $Sz = ($SSHRinv * $Unit)->length();
my $Sinv = $M->shadow(); $Sinv->zero(); # Create and zero the inverse Scaling Matrix
$Sinv->assign(1, 1, $Sx); $Sx = 1/$Sx;
$Sinv->assign(2, 2, $Sy); $Sy = 1/$Sy;
$Sinv->assign(3, 3, $Sz); $Sz = 1/$Sz;
# SHEARS - [M] = inv[T][T]inv[S][S][SH][R] = [SH][R]
# We assume the shear matrix: SH [ 1 0 0 0 ]
# where x' = x [ a 1 0 0 ]
# y' = ax + y [ b c 1 0 ]
# z' = bx + cy + z [ 0 0 0 1 ]
#
# However as M at this point is in fact [SH][R]
# we can extract a, b and c as such:
#
# let [ M1 ]
# [ M2 ] = [SH][R]
# [ M3 ]
#
# thus:
#
# a = (M2 . M1) / |M1|^2
# b = (M3 . M1) / |M1|^2
# c = (M3 . T) / |T|^2 where T = M2 - (a . M1)
#
# We could also use the determinant to determine whether we have an
# Orthogonal matrix and thus don;t have shears, but we don't do this yet....
$M = $Sinv * $M;
# check determinant for "sheariness" if det != 0 shears exist.
# my $det = $M->decompose_LR()->det_LR();
my $M1 = ~$M->row(1);
my $M2 = ~$M->row(2);
my $M3 = ~$M->row(3);
$SHa = $M2->scalar_product($M1) / $M1->scalar_product($M1);
$SHb = $M3->scalar_product($M1) / $M1->scalar_product($M1);
my $TMP = $M2 - ($SHa * $M1);
$SHc = $M3->scalar_product($TMP) / $TMP->scalar_product($TMP);
my $SH = $M->shadow(); $SH->one(); # Create and zero the Shear Matrix
$SH->assign(2, 1, $SHa);
$SH->assign(3, 1, $SHb);
$SH->assign(3, 2, $SHc);
# ROTATIONS - [M] = inv[T][T]inv[S][S]inv[SH][SH][R] = [R]
# We assume cy is positive to ensure we get one of the 2 possible solutions
# where rotations are between -pi and pi.
#
# Here we deduce Rx, Ry and Rz by virtue or the fact that the rotation
# matrix is as follows.
#
# R = [ cos(Ry)*cos(Rz) <stuff> <stuff> 0 ]
# [ cos(Ry)*sin(Rz) <stuff> <stuff> 0 ]
# [ sin(Ry) sin(Rx)*cos(Ry) cos(Rx)*cos(Ry) 0 ]
# [ 0 0 0 0 ]
#
# Then the quadrant of the angle must be deduced by the sign of
# cos and sin for the particular rotation.
$M = $SH->decompose_LR()->invert_LR() * $M;
# Get Y Rotation and check that we aren't up a creek without a paddle
my $sy = $M->element(3, 1);
if (abs($sy) == 1) { die "cos X = 0. I haven't solved this yet...\n"; }
$Ry = asin($sy);
# Get X Rotation
my $cy = cos($Ry);
my $sx = $M->element(3, 2) / $cy;
my $cx = $M->element(3, 3) / $cy;
$Rx = asin($sx);
if ($cx < 0){
if ($sx > 0){ $Rx = pi() - $Rx; } # quadrant 2
else { $Rx = -pi() - $Rx; } # quadrant 3
}
# Get Z Rotation
my $cz = $M->element(1, 1) / $cy;
my $sz = $M->element(2, 1) / $cy;
$Rz = asin($sz);
if ($cz < 0){
if ($sz > 0){ $Rz = pi() - $Rz; } # quadrant 2
else { $Rz = -pi() - $Rz; } # quadrant 3
}
# If verbose do a bit of checking and output the remainder which should
# be the identity matrix or close to it
if ($verbose){
my $RX = $M->shadow(); $RX->one(); # Create and zero the X Rotation Matrix
$RX->assign(2, 2, cos($Rx)); $RX->assign(2, 3, -sin($Rx));
$RX->assign(3, 2, sin($Rx)); $RX->assign(3, 3, cos($Rx));
my $RY = $M->shadow(); $RY->one(); # Create and zero the Y Rotation Matrix
$RY->assign(1, 1, cos($Ry)); $RY->assign(1, 3, -sin($Ry));
$RY->assign(3, 1, sin($Ry)); $RY->assign(3, 3, cos($Ry));
my $RZ = $M->shadow(); $RZ->one(); # Create and zero the Z Rotation Matrix
$RZ->assign(1, 1, cos($Rz)); $RZ->assign(1, 2, -sin($Rz));
$RZ->assign(2, 1, sin($Rz)); $RZ->assign(2, 2, cos($Rz));
my $RZYXinv = ($RZ * $RY * $RX)->decompose_LR()->invert_LR();
print "Remainder:\n" . ($RZYXinv * $M);
}
@$Scale[0] = $Sx; @$Scale[1] = $Sy; @$Scale[2] = $Sz;
@$Shear[0] = $SHa; @$Shear[1] = $SHb; @$Shear[2] = $SHc;
@$Rotn[0] = $Rx; @$Rotn[1] = $Ry; @$Rotn[2] = $Rz;
}
# Creates a 4x4 transformation matrix $M using the input
# Translations, scales, shears and rotations (or not)
sub create_transformation_matrix{
my($Trans, $Scale, $Shear, $Rotn) = @_;
# set a few defaults
my $c;
for ($c = 0; $c < 3; $c ++){
if (!defined @$Trans[$c]){ @$Trans[$c] = 0; }
if (!defined @$Scale[$c]){ @$Scale[$c] = 1; }
if (!defined @$Shear[$c]){ @$Shear[$c] = 0; }
if (!defined @$Rotn[$c] ){ @$Rotn[$c] = 0; }
}
my $M = Math::MatrixReal->new(4, 4); $M->one();
$M->assign(1, 4, @$Trans[0]);
$M->assign(2, 4, @$Trans[1]);
$M->assign(3, 4, @$Trans[2]);
$M->assign(1, 1, @$Scale[0]);
$M->assign(2, 2, @$Scale[1]);
$M->assign(3, 3, @$Scale[2]);
my $SH = $M->shadow(); $SH->one(); # Create and zero the Shear Matrix
$SH->assign(2, 1, @$Shear[0]);
$SH->assign(3, 1, @$Shear[1]);
$SH->assign(3, 2, @$Shear[2]);
my $RX = $M->shadow(); $RX->one(); # Create and zero the X Rotation Matrix
$RX->assign(2, 2, cos(@$Rotn[0])); $RX->assign(2, 3, -sin(@$Rotn[0]));
$RX->assign(3, 2, sin(@$Rotn[0])); $RX->assign(3, 3, cos(@$Rotn[0]));
my $RY = $M->shadow(); $RY->one(); # Create and zero the Y Rotation Matrix
$RY->assign(1, 1, cos(@$Rotn[1])); $RY->assign(1, 3, -sin(@$Rotn[1]));
$RY->assign(3, 1, sin(@$Rotn[1])); $RY->assign(3, 3, cos(@$Rotn[1]));
my $RZ = $M->shadow(); $RZ->one(); # Create and zero the Z Rotation Matrix
$RZ->assign(1, 1, cos(@$Rotn[2])); $RZ->assign(1, 2, -sin(@$Rotn[2]));
$RZ->assign(2, 1, sin(@$Rotn[2])); $RZ->assign(2, 2, cos(@$Rotn[2]));
return $M * $SH * $RZ * $RY * $RX;
}
sub print_transformation_matrix{
my($M, $name) = @_;
my (@Trans, @Scale, @Shear, @Rotn, @Rotnd);
print "$name:\n$M";
decompose_transformation_matrix($M, \@Trans, \@Scale, \@Shear, \@Rotn);
foreach (@Rotn){ push(@Rotnd, rad2deg($_)); }
printf("Translation: %10.5f %10.5f %10.5f\n", @Trans);
printf("Rotation: %10.5f %10.5f %10.5f\n", @Rotnd);
printf("Scale: %10.5f %10.5f %10.5f\n", @Scale);
printf("Shear: %10.5f %10.5f %10.5f\n", @Shear);
}