#!/usr/bin/perl

# Copyright 2015 O. Sotolongo <osotolongo@fundacioace.com>

use strict; use warnings;
use File::Slurp qw(read_file);
use Data::Dump qw(dump);
use NEURO qw(populate check_subj load_study print_help get_petdata get_pair achtung shit_done);

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

unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/dcm_moco.hlp'; exit;}

my %std = load_study($study);

my $data_dir=$std{'DATA'};
my $ifile = 'ep2d_pace_moco_p2.loc';
my $dest_dir = 'fmri_conv';
my %locs = map { my ( $key, $value ) = split " "; $key => $value} read_file $data_dir.'/'.$ifile;

foreach my $subject (sort keys %locs) {
	my ($short) = $subject =~ /0(.*)/;
	#print "$short\n";
	my $orig = '"/nas/corachan/facehbi/F'.$short.'/Serie('.$locs{$subject}.')/Img00001.dcm"';
	#print "$orig\n";
	my $order = 'mkdir '.$data_dir.'/'.$dest_dir.'/f'.$short.' && dcm2nii -o '.$data_dir.'/'.$dest_dir.'/f'.$short.' '.$orig;
	print "$order\n";
	system($order);
}