add icbm_make_templates.pl

ChangeLog

@@ -1,3 +1,6 @@
+2007-01-30  Claude Lepage <[email protected]>
+	* add icbm_make_templates.pl 
+
 2006-06-22  Claude Lepage <[email protected]>
 	* modify multispectral_stx_registration for new pipeline
         * use model icbm_avg_152_t1_tal_nlin_symmetric_VI in nlfit_smr

NEWS

@@ -1,3 +1,8 @@
+        New in Release 1.6.4
+        --------------------
+* Add icbm_make_templates.pl
+  (not yet packaged as of Jan-30-2007)
+
         New in Release 1.6.3
         --------------------
 * Modification of multispectral_stx_registration for new pipeline

configure.ac

@@ -1,6 +1,6 @@
 dnl Process this file with autoconf to produce a configure script.
 
-AC_INIT(conglomerate, 1.6.3, [email protected])
+AC_INIT(conglomerate, 1.6.4, [email protected])
 AC_CONFIG_SRCDIR([surface_mask2.c])
 AM_INIT_AUTOMAKE
 AC_CONFIG_HEADERS([config.h])

icbm_make_templates.pl

@@ -0,0 +1,74 @@
+#! /usr/bin/env perl
+
+# Generate templates for a given model (inspired by icbm_make_templates 
+# from Neelin).
+#
+# Claude Lepage - [email protected]
+#
+# Permission to use, copy, modify, and distribute this software and its
+# documentation for any purpose and without fee is hereby granted,
+# provided that the above copyright notice appear in all copies.  The
+# author and the University of Queensland make no representations about the
+# suitability of this software for any purpose.  It is provided "as is"
+# without express or implied warranty.
+
+use strict;
+use warnings "all";
+use File::Temp qw/ tempdir /;
+
+# Output prefix
+my $PREFIX = "icbm_nlin_template";
+
+# Dimensions
+my $XSTART = -96;
+my $YSTART = -132;
+my $ZSTART = -78;
+
+my $XCENTER = 0;
+my $YCENTER = -18;
+my $ZCENTER = 18;
+
+my $XLEN = 192;
+my $YLEN = 228;
+my $ZLEN = 192;
+
+my @spacings = ( "0.50", "0.75", "1.00", "1.50", "2.00", "3.00", "4.00", "6.00" );
+
+my $date = `date`;
+chomp( $date );
+
+# make tmpfile
+my $tmpdir = &tempdir( "template-XXXX", TMPDIR => 1, CLEANUP => 1 );
+
+# Generate the templates at each size
+
+for( my $i = 0;  $i < @spacings;  $i++ ) {
+
+  my $dx = $XLEN / $spacings[$i] + 1;
+  my $dy = $YLEN / $spacings[$i] + 1;
+  my $dz = $ZLEN / $spacings[$i] + 1;
+
+  my $list = "$dx $dy $dz -xstart $XSTART -ystart $YSTART -zstart $ZSTART " .
+             "-xstep $spacings[$i] -ystep $spacings[$i] -zstep $spacings[$i] " .
+             "-xdircos 1 0 0 -ydircos 0 1 0 -zdircos 0 0 1";
+  print "creating template ${PREFIX}_${spacings[$i]}mm.mnc...\n";
+
+  open PIPE, ">${tmpdir}/template_${spacings[$i]}.sh";
+  print PIPE "#! /bin/csh -f\n";
+  print PIPE "limit filesize 4k\n";
+  print PIPE "rawtominc -clobber -byte -input /dev/zero ${PREFIX}_${spacings[$i]}mm.mnc " .
+             "$list -transverse -sattribute xspace:spacetype=talairach_ " .
+             "-sattribute yspace:spacetype=talairach_ -sattribute zspace:spacetype=talairach_ " .
+             "-sattribute xspace:units=mm -sattribute yspace:units=mm -sattribute zspace:units=mm " .
+             "-sattribute \':history=$date >>> icbm_make_templates\'\n";
+  close PIPE;
+  system( "chmod u+x ${tmpdir}/template_${spacings[$i]}.sh" );
+  system( "${tmpdir}/template_${spacings[$i]}.sh" );
+  unlink( "${tmpdir}/template_${spacings[$i]}.sh" );
+}
+
+
+sub run { 
+  system(@_) == 0 or die;
+}
+