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* mni_perllib changes to suppress_fat
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@andrewjanke
andrewjanke committed Jul 27, 2006
1 parent 9c6bac1 commit 63bd355
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Showing 2 changed files with 35 additions and 46 deletions.
5 changes: 3 additions & 2 deletions mritotal_suppress.in
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Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,9 @@
# express or implied warranty.
#----------------------------------------------------------------------------
#$RCSfile: mritotal_suppress.in,v $
#$Revision: 1.2 $
#$Revision: 1.3 $
#$Author: rotor $
#$Date: 2006-07-27 03:45:32 $
#$Date: 2006-07-27 06:13:28 $
#$State: Exp $
#---------------------------------------------------------------------------

Expand All @@ -26,6 +26,7 @@ use FindBin;
use MNI::Startup qw(nocputimes);
use MNI::Spawn;
use MNI::FileUtilities qw(check_output_dirs);
use MNI::PathUtilities qw(split_path);

# ------------------------------ start here
&Initialize;
Expand Down
76 changes: 32 additions & 44 deletions suppress_fat.in
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Original file line number Diff line number Diff line change
Expand Up @@ -14,32 +14,28 @@
# express or implied warranty.
#----------------------------------------------------------------------------
#$RCSfile: suppress_fat.in,v $
#$Revision: 1.1 $
#$Author: claude $
#$Date: 2006-05-04 19:40:04 $
#$Revision: 1.2 $
#$Author: rotor $
#$Date: 2006-07-27 06:13:28 $
#$State: Exp $
#---------------------------------------------------------------------------

use FindBin;
use Startup;
use JobControl;
use Getopt::Tabular;
#use MNI::DataDir;
use FindBin;

require "file_utilities.pl";
require "path_utilities.pl";
require "minc_utilities.pl";
require "numeric_utilities.pl";
require "volume_heuristics.pl";
use MNI::Startup qw(nocputimes);
use MNI::Spawn;
use MNI::FileUtilities qw(check_output_dirs check_files);
use MNI::PathUtilities qw(split_path replace_dir);
use MNI::MincUtilities qw(volume_minmax);

# ------------------------------ start here
&Startup;

&Initialize;

# ------------------------------ get the input file

($originputfile) = &uncompress ($TmpDir, $inputfile);
$originputfile = $inputfile;

# ------------------------------ build a brain mask on the native data volume

Expand Down Expand Up @@ -71,21 +67,20 @@ sub Initialize
$Version = "@VERSION@";
$LongVersion = "version ${Version}: slightly tested perl code. Beware!";

&SelfAnnounce ("STDOUT") if $Verbose && ! -t "STDOUT";
&self_announce() if $Verbose;

$Verbose = 1;
$Execute = 1;
$Clobber = 0;
$Debug = 0;

$KeepTmp = 0;
&JobControl::SetOptions ("ErrorAction", "fatal");
&MNI::Spawn::SetOptions (err_action => 'fatal' );

$Transform = undef;
$ModelDir = 'avg305';
$ModelDir = 'mni_autoreg';
$ModelBase = undef;
$BrainMask = "$FindBin::Bin/../share/$ModelDir/" . "average_305_mask_1mm.mnc";
#$BrainMask = MNI::DataDir::dir($ModelDir) . "average_305_mask_1mm.mnc";
$BrainMask = "$FindBin::Bin/../share/$ModelDir/icbm_avg_152_t1_tal_lin_mask.mnc";

my $usage = <<USAGE;
Usage: $ProgramName [options] <fat.mnc> <lite.mnc>
Expand Down Expand Up @@ -125,7 +120,7 @@ HELP
&Getopt::Tabular::SetHelp ($help, $usage);

my (@argv) = @ARGV;
&GetOptions (\@ArgInfo, \@argv) || &Fatal ();
&GetOptions (\@ArgInfo, \@argv) || exit();

if (@argv == 2) {
($inputfile, $outputfile) = @argv;
Expand All @@ -138,15 +133,12 @@ HELP
}

# Look for required programs
$MincMath = &FindProgram ("mincmath");
$XfmInvert = &FindProgram ("xfminvert");
$MincResample = &FindProgram ("mincresample");
$MincLookup = &FindProgram ("minclookup");
$VolumeStats = &FindProgram ("volume_stats");
$VolumeHist = &FindProgram ("volume_hist");

die unless ($MincMath && $XfmInvert && $MincResample && $VolumeStats &&
$VolumeHist && $MincLookup);
$MincMath = "mincmath";
$XfmInvert = "xfminvert";
$MincResample = "mincresample";
$MincLookup = "minclookup";
$VolumeStats = "volume_stats";
$VolumeHist = "volume_hist";

# They were found, so add options according to
# $Debug, $Verbose, $Clobber flags
Expand All @@ -161,7 +153,6 @@ HELP

if (! -d $ModelDir) {
$ModelDir = "$FindBin::Bin/../share/$ModelDir/";
#$ModelDir = MNI::DataDir::dir($ModelDir);
}

if (defined($ModelBase)) {
Expand All @@ -172,10 +163,10 @@ HELP
die "$outputfile already exists (use -clobber to overwrite)\n";
}

die if (defined($Transform) && !CheckFiles($Transform));
die if (!CheckFiles($inputfile, $BrainMask));
die if (defined($Transform) && !check_files($Transform));
die if (!check_files($inputfile, $BrainMask));

&CheckOutputDirs ($TmpDir) if $Execute;
&check_output_dirs ($TmpDir) if $Execute;
}

# ------------------------------
Expand All @@ -201,9 +192,9 @@ sub remap_intensities {
$f_min, $f_max, $f_mean, $f_std, $f1, $t1, $t2,
$lut, $lower, $upper, $min_range, $max_range);

$filebase = (&SplitPath ($brain))[1];
$filebase = (&split_path ($brain))[1];
$new_brain = "${TmpDir}/${filebase}_remapped.mnc";
$filebase = (&SplitPath ($nonbrain))[1];
$filebase = (&split_path ($nonbrain))[1];
$new_nonbrain = "${TmpDir}/${filebase}_remapped.mnc";

# Get brain and nonbrain intensity stats
Expand All @@ -213,9 +204,6 @@ sub remap_intensities {
print "Brain: min = $min, max = $max, mean = $mean, std = $std\n" if ($Debug) ;
print "Brain: range min = $min_range, max = $max_range\n" if ($Debug);

# ($nb_min, $nb_max, $nb_mean, $nb_std) = get_masked_volume_stats( $nonbrain, $mask );
# print "Non-Brain: min = $min, max = $max, mean = $mean, std = $std\n" if ($Debug) ;

$f_mean = $mean / $max_range ;
$f1 = ($mean + 5 * $std) / $max_range;
$f1 = 1.0 if ($f1 > 1.0);
Expand Down Expand Up @@ -266,8 +254,8 @@ sub get_masked_volume_stats{

my($output, $result);

($result, $output) = &Spawn ("$VolumeStats -min -max -mean -stddev -quiet -mask $mask ${file}","-");

$output = `$VolumeStats -min -max -mean -stddev -quiet -mask $mask $file`;
split("\n",$output);
}

Expand All @@ -293,7 +281,7 @@ sub compute_thresholds{
my ($file, $mask, $low_lim, $up_lim) = @_;
my ($filebase, $upper, $lower, $out_histo, $int, $cnt, $s_int, $s_cnt, $i, $s);

$filebase = (&SplitPath ($file))[1];
$filebase = (&split_path ($file))[1];

$out_histo = "${TmpDir}/${filebase}.histo.txt";

Expand Down Expand Up @@ -364,7 +352,7 @@ sub build_native_brain_mask {

my ($result, $inverse);
# get the file basename, without directory
$filebase = (&SplitPath ($native_mnc))[1];
$filebase = (&split_path ($native_mnc))[1];

$result = "${TmpDir}/${filebase}_native_brain_mask.mnc";
$inverse = "${TmpDir}/${filebase}_inv.xfm";
Expand Down Expand Up @@ -397,15 +385,15 @@ sub build_native_brain_mask {
sub mask_data {
my ($file, $mask, $invert_flag, $label) = @_;

my($filebase) = (&SplitPath ($file))[1];
my($filebase) = (&split_path ($file))[1];
my($result) = "${TmpDir}/${filebase}_${label}.mnc";

if (-e "$result") {
print ("file $result already exists\n");
}
else {
if ($invert_flag) {
my($inverted_mask) = &ReplaceDir($TmpDir, $mask);
my($inverted_mask) = &replace_dir($TmpDir, $mask);
$inverted_mask .= "_inv";

if (-e $inverted_mask) {
Expand Down

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