#!/usr/bin/perl
use strict; use warnings;
use File::Slurp qw(read_file);
use File::Find::Rule;
use File::Basename qw(basename);
use Data::Dump qw(dump);
use File::Copy::Recursive qw(dirmove);

use NEURO qw(load_study print_help achtung shit_done);



@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/fsl2fs.hlp'; exit;}
}
my $study = shift;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/make_pet_report.hlp'; exit;}

my %std = load_study($study);

#Run this script ONLY on "Detritus"
#or change the paths to the correct ones

my $w_dir=$std{'WORKING'};
my $d_dir=$std{'DATA'};

# Redirect ouput to logfile (do it only when everything is fine)
#my $debug = "$d_dir/.debug_report.log";
#open STDOUT, ">$debug" or die "Can't redirect stdout";
#open STDERR, ">&STDOUT" or die "Can't dup stdout";

my $order = "slicesdir -o ";
my @names = find(file => 'name' => "*_b0_to_t1.nii.gz", in => $w_dir);
foreach my $name (sort @names){
        (my $tmpl = $name) =~ s/_b0_to_t1/_t1_reoriented/;
        $order .= $name.' '.$tmpl." ";
}
chdir $w_dir;
system($order);
print "$order\n";
dirmove('slicesdir', 'dtis');