Hi, i luckily solved the problem while having another look at the data with
imageJ. It was a problem with the 'endianess'. I was running dcm2nii on a
non-intel mac. That caused the data to be processed as BigEndian.
I contacted Chris Rorden and he said he will look into it.
Michael
On Tue, 12 Aug 2008 10:58:11 +0100, Colm G. Connolly <[log in to unmask]>
wrote:
>
>On 11 Aug 2008, at 22:53, Michael Scheel wrote:
>
>> (PAR v4.1 not yet fully supported) and strange conversion
>> results - intensity values for an anatomical scan range from
>> -500.000 to
>> 500.000.
>> Any ideas? How can I convert my PAR/REC files into an fsl format?
>
>If you can export PAR/REC V4.1 then chances are that you can export
>the data as NIfTI and so obviate the need to do the conversion in the
>first place. Alternatively, you can download and install AFNI and use
>the 3dPAR2AFNI.pl script attached to this email to perform the
>conversion from PAR/REC to NIfTI.
>
>#!/usr/bin/perl -w
>#3dPARtoANALYZE somefile.par
>
># This file is a modified version of this file
>#
http://www.cdfi.uab.edu/cdfi/Documents/6740FF06-1993-4EAE-8CF7-18CBCA3D78B6.html
>
>use strict;
>use Getopt::Std;
>use Cwd;
>
>my %Options = ();
>my $ok = getopts("hsnvg24o:a", \%Options);
># codes indicating the cardinal plane in which the data was acquired
>my $TRANSVERSE = 1;
>my $SAGITTAL = 2;
>my $CORONAL = 3;
>
>sub usage(){
>
> print "3dPAR2ANFI\n";
> print "Version: 2008/08/11 15:12\n\n";
> print "Command line Options:\n";
> print "-h This help message.\n";
> print "-v Be verbose in operation.\n";
> print "-s Skip the outliers test when converting 4D files\n";
> print " The default is to perform the outliers test.\n";
> print "-n Output NIfTI files instead of HEAD/BRIK.\n";
> print " The default is create HEAD/BRIK files.\n";
> print "-a Output ANALYZE files instead of HEAD/BRIK.\n";
> print "-o The name of the directory where the created files should be\n";
> print " placed. If this directory does not exist the program exits\n";
> print " without performing any conversion.\n";
> print " The default is to place created files in the same directory\n";
> print " as the PAR files.\n";
> print "-g Gzip the files created.\n";
> print " The default is not to gzip the files.\n";
> print "-2 2-Byte-swap the files created.\n";
> print " The default is not to 2 byte-swap.\n";
> print "-4 4-Byte-swap the files created.\n";
> print " The default is not to 4 byte-swap.\n\n";
>
> print "Sample invocations:\n";
> print "3dPAR2AFNI subject1.PAR\n";
> print " Converts the file subject1.PAR file to subject1+orig.{HEAD,BRIK}\n";
> print "3dPAR2AFNI -s subject1.PAR\n";
> print " Same as above but skip the outlier test\n";
> print "3dPAR2AFNI -n subject1.PAR\n";
> print " Converts the file subject1.PAR file to subject1.nii\n";
> print "3dPAR2AFNI -n -s subject1.PAR\n";
> print " Same as above but skip the outlier test\n";
> print "3dPAR2AFNI -n -s -o ~/tmp subject1.PAR\n";
> print " Same as above but skip the outlier test and place the\n";
> print " created NIfTI files in ~/tmp\n";
> print "3dPAR2AFNI -n -s -o ~/tmp *.PAR\n";
> print " Converts all the PAR/REC files in the current directory to\n";
> print " NIfTI files, skip the outlier test and place the created\n";
> print " NIfTI files in ~/tmp\n";
>
> exit;
>}
>
>sub convertPar($) {
> $,=" ";
> $\="\n";
> my $verbose = $Options{"v"};
> my $skipOutliers = $Options{"s"};
> my $nifti = $Options{"n"};
> my $analyze = $Options{"a"};
> my $gzip = $Options{"g"};
> my $twoSwap = $Options{"2"};
> my $fourSwap = $Options{"4"};
> my $outputDirectory = $Options{"o"};
> my $outliers="";
> my $parFile = shift;
> my $sliceOrder = undef;
> my ($rootname, $extension, %fov, %angulation, %origin, $slices, $tr,
$volumes, $bitdepth, %reconres, $prefixargs);
> my ($timeargs, $totalslices, $anterior, $posterior, $foot, $head, $right,
$left, $FOVargs, $filespec, $session);
>
> # the maximum number of pieces of header info needed from the PAR file
> my $maxHeaders = 9;
>
> if ($outputDirectory){
> if ( ! -d $outputDirectory ) {
> print "$outputDirectory does not exist. Exiting!\n";
> exit;
> }
> $outputDirectory = Cwd::abs_path($outputDirectory);
> }
>
> if ($verbose) {
> print "Skipping outliers test\nOutput file will be NIfTI format\n";
> }
>
> if ($parFile =~ /([A-Za-z_0-9]+)\.([Pp][Aa][Rr])$/) {
> $rootname=$1;
> $extension=$2;
> }
>
> # parse PAR file.
> my $lineCount=0;
>
> open(PFH, $parFile) || die "Unable to open $parFile for reading: $!.\n";
> my @buffer = ();
> my $foundAllHeaderInfo = 0;
> while (<PFH>) {
> chomp; # strip record separator
>
> push (@buffer, $_);
> if ($#buffer > 2){
> shift @buffer;
> }
> #print "foundAllHeaderInfo is $foundAllHeaderInfo\n";
> if ($foundAllHeaderInfo < $maxHeaders) {
> #print $_;
> # file version
> if
(/#\s+CLINICAL\s+TRYOUT\s+Research\s+image\s+export\s+tool\s+V(\d+(\.\d+)?)/) {
> my $fileVersion = $1;
> if ($verbose) {
> print "This PAR file is from research image export tool version
$fileVersion\n";
> }
> if (!($fileVersion eq "4" or $fileVersion eq "4.2")) {
> print "This program has only been tested to work with Version 4
or 4.2 PAR/REC files. Exiting.";
> exit;
> }
> $foundAllHeaderInfo++; #print "foundAllHeaderInfo 1\n"; #1
> }
>
> # field of view
> if (/FOV \((..),(..),(..)\)
\[.*\].*:\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)/) {
> $fov{$1}=$4;
> $fov{$2}=$5;
> $fov{$3}=$6;
> $foundAllHeaderInfo++; #print "foundAllHeaderInfo 2\n";#2
> }
> # matrix size
>
> # angulation
> if (/Angulation
midslice\((..),(..),(..)\)\[.*\].*:\s*(-?\d+\.\d+)\s*(-?\d+\.\d+)\s*(-?\d+\.\d+)/)
{
> $angulation{$1}=$4;
> $angulation{$2}=$5;
> $angulation{$3}=$6;
> $foundAllHeaderInfo++; #print "foundAllHeaderInfo 3\n";#3
> }
>
> # distance from origin of FOV center
> if (/Off Centre midslice\((..),(..),(..)\)
\[.*\].*:\s*(-?\d+\.\d+)\s*(-?\d+\.\d+)\s*(-?\d+\.\d+)/) {
> $origin{$1}=$4;
> $origin{$2}=$5;
> $origin{$3}=$6;
> $foundAllHeaderInfo++; #print "foundAllHeaderInfo 5\n";; #5
> }
>
> # number of slices
> if (/number of slices.*:\s*(\d+)/) {
> $slices=$1;
> $foundAllHeaderInfo++; #print "foundAllHeaderInfo 6\n"; #6
> }
>
> # TR
> if (/Repetition time.*:\s*(\d+\.\d+)/) {
> $tr=$1;
> $foundAllHeaderInfo++; #print "foundAllHeaderInfo 7\n"; #7
> }
> # number of volumes
> if (/number of dynamics.*:\s*(\d+)/) {
> $volumes=$1;
> $foundAllHeaderInfo++; #print "foundAllHeaderInfo 8\n"; #8
> }
>
> # matrix size
>
> # this branch of the must execute twice inorder to determine the
> # slice order. on the first line of image information the
> # dynamic number will naturally be 1. it is only by looking at
> # the second line that we can determine whether the data is in
> # tz or zt order. maxHeaders must be set to be one higher than
> # the actual number of pieces of header information we
> # need. this allows this branch to execute twice because it will
> # match each line in the image information section.
>
> if
(/\s*\d+\s+\d+\s+(\d+)\s+(?:\d+\s+){4}(\d+)\s+\d+\s+(\d+)\s+(\d+)\s+(?:[+-]?(?:\d+\.\d+|\d+\.|\.\d+|\d+)(?:[eE][+-]?\d+)?\s+){14}(\d{1}).*/)
{
> my $dynamicNumber = $1;
> $bitdepth=$2;
> $reconres{"x"}=$3;
> $reconres{"y"}=$4;
> $reconres{"orientation"}=$5;
> $foundAllHeaderInfo++; #print "foundAllHeaderInfo 9\n"; #9
> if ($verbose) {
> print "*** The dynamic number is $dynamicNumber";
> }
> if ($dynamicNumber != 1 ) {
> $sliceOrder = "tz";
> }
> else {
> $sliceOrder = "zt";
> }
> }
> }
> # don't try to be clever and put a else { last; } here. if you do
> # that the script does not read the rest of the par file and
> # consequently cannot determine the number of volumes. moral of
> # the story the script must read every line in the PAR file.
> $lineCount++;
> } # end of while (<PFH>)
>
> if (shift(@buffer) =~ /\s*\d*\s+\d*\s+\d*\s+\d*\s+\d*\s+\d*\s+(\d*).*/){
> my $numberOfImages = $1 + 1;
> if ($verbose) {
> print "*** Number of images is $numberOfImages";
> }
>
> if ($numberOfImages / $slices != $volumes) {
> print "*** WARNING: The number of volumes from the PAR header does
not match the number of slices times the number of images!";
> $volumes = $numberOfImages / $slices;
> print "*** WARNING: Resetting the number of volumes to be the number
of slices times the number of images ($volumes).";
> }
> }
>
> close(PFH);
>
> if ($verbose) {
> print "$rootname.$extension";
> print "*** Field of View ***";
> print "ap=$fov{ap}";
> print "fh=$fov{fh}";
> print "rl=$fov{rl}";
> print "*** Reconstruction Matrix ***";
> print "x=$reconres{x}";
> print "y=$reconres{y}";
> print "orientation=$reconres{orientation}";
> print "*** Angulation ***";
> print "ap=$angulation{ap}";
> print "fh=$angulation{fh}";
> print "rl=$angulation{rl}";
> print "*** Origin ***";
> print "ap=$origin{ap}";
> print "fh=$origin{fh}";
> print "rl=$origin{rl}";
> print "*** Slices = $slices ***";
> print "*** Bit Depth = $bitdepth ***";
> print "*** TR = $tr ***";
> print "*** Slice order is $sliceOrder";
> }
>
> # -----------calculate values and args for AFNI to3d to convert REC file
> #
> if ($outputDirectory) {
> $session = "-session $outputDirectory/";
> }
> else {
> $session = "";
> }
>
> if ($nifti) {
> $prefixargs = "-prefix $rootname.nii";
> }
> else {
> $prefixargs = "-prefix $rootname";
> }
>
> my $swap = "";
> if ($twoSwap) {
> $swap = "-2swap";
> }
> elsif ($fourSwap) {
> $swap = "-4swap";
> }
>
> # generate time args for func or anat
> $timeargs = "";
> $totalslices = $slices;
>
> if ($volumes > 1) {
> if ($verbose) {
> print "$volumes timepoints";
> }
> if ($sliceOrder eq "tz" ) {
> $timeargs = "-time:tz $volumes $slices ${tr}ms zero";
> }
> elsif ($sliceOrder eq "zt") {
> $timeargs = "-time:zt $slices $volumes ${tr}ms zero";
> }
> $totalslices=$volumes*$slices;
> if ($skipOutliers) {
> $outliers="-skip_outliers";
> }
> }
>
> #calculate FOV args
> $anterior = abs($origin{ap}-$fov{ap}/2);
> $posterior= abs($origin{ap}+$fov{ap}/2);
> $foot = abs($origin{fh}-$fov{fh}/2);
> $head = abs($origin{fh}+$fov{fh}/2);
> $right = abs($origin{rl}-$fov{rl}/2);
> $left = abs($origin{rl}+$fov{rl}/2);
>
> if ($reconres{orientation} == $TRANSVERSE ) {
> if ($verbose) {
> print "Data was acquired in the TRANSVERSE plane\n";
> }
> $FOVargs = "-xFOV ${right}R-${left}L -yFOV ${anterior}A-${posterior}P
-zFOV ${foot}I-${head}S";
> } elsif ($reconres{orientation} == $SAGITTAL ) {
> #$FOVargs = "-xFOV ${right}R-${left}L -yFOV ${anterior}A-${posterior}P
-zFOV ${foot}I-${head}S";
> print "** Sorry this program cannot convert files that were acquired in
the SAGITTAL plane\n";
> return;
> }
> elsif ($reconres{orientation} == $CORONAL ) {
> #$FOVargs = "-xFOV ${right}R-${left}L -yFOV ${anterior}A-${posterior}P
-zFOV ${foot}I-${head}S";
> print "*** Sorry this program cannot convert files that were acquired
in the CORONAL plane\n";
> return;
> }
>
> #file specification
> my $recextension="rec";
> if ($extension =~ /PAR/) {
> $recextension="REC";
> }
> $filespec =
"3D:-1:0:$reconres{x}:$reconres{y}:$totalslices:$rootname.$recextension";
> my $fileSize = -s "$rootname.$recextension";
>
> if ( $fileSize > 0 ) {
> # to3d command
> print my $command="to3d $session $swap $outliers $prefixargs $timeargs
$FOVargs $filespec";
> system $command;
> if ($analyze) {
> print my $command="3dAFNItoANALYZE $rootname $rootname+orig.HEAD";
> system $command;
> print $command="rm -f $rootname+orig.{HEAD,BRIK}";
> system $command;
> }
> if ($gzip) {
> if ($nifti) {
> $command="gzip -9v $rootname.nii";
> } elsif ($analyze) {
> $command="gzip -9v $rootname.img";
> } else {
> $command="gzip -9v $rootname+orig.BRIK";
> }
> print $command;
> system $command;
> }
> } else {
> print "Skipping $parFile: The corresponding REC file is 0 bytes in
length\n";
>
> }
>}
>
>sub main() {
> my $argCount = $#ARGV + 1;
> usage() if $Options{"h"} or $argCount < 1;
>
> foreach my $parFile (@ARGV) {
> print "*** Converting $parFile\n";
> convertPar($parFile);
> }
>}
>
>main();
>
>
>
>Regards,
>--
>Dr Colm G. Connolly
>School of Psychology and Institute of Neuroscience
>The Lloyd Building
>University of Dublin
>Trinity College, Dublin 2, Éire
>Fax: +353-1-671-3183
>
>Please note that electronic mail to, from or within the Trinity
>College Dublin, may be the
>subject of a request under the Freedom of Information Act.
>
>
>
>
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