#!/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 NEURO4 qw(load_project print_help shit_done);

@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/make_dti_report.hlp'; exit;}
}
my $study = shift;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/make_dti_report.hlp'; exit;}
my %std = load_project($study);
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' => "*mni_to_b0.nii.gz", in => $w_dir);
foreach my $name (sort @names){
	(my $warped = $name) =~ s/mni_to_b0/hifi_b0/; 
	$order .= $warped.' '.$name." ";
}
chdir $w_dir;
system($order);
print "$order\n";
dirmove('slicesdir', 'dtis');