#!/usr/bin/perl

use strict;
use warnings;
use NEURO qw(load_study);
use Data::Dump qw(dump);
use File::Find::Rule;

my $study = "facehbi";
my %std = load_study($study);
my $src_dir = "/nas/clinic/facehbi";
my $output_dir = $std{'PET-FBB'};
my @other_exts = ("nii.gz","json");

opendir(my $dh, $src_dir) || die "Can't opendir $src_dir: $!";
my @adqs = grep {/^[A-Za-z]/} readdir($dh);
closedir $dh;

foreach my $adq (sort @adqs) {
	(my $subject = $adq) =~ s/.*-F(.*)B$/0$1/;
	my $order = 'dcm2niix -z y -o '.$std{'DATA'}.'/tmp/ '.$src_dir.'/'.$adq.'/DICOM';
	print "$order\n";
	system($order);
	my @conv_files = find(file => 'name' => "*.nii.gz", in => $std{'DATA'}.'/tmp/');
	foreach my $nii_file (@conv_files){
		$order = 'fslinfo '.$nii_file;
		my %xinfo;
		foreach (qx/$order/){
			my ( $key, $value ) = /(\S+)\s+(\S+)\s*.*/;
			$xinfo{$key} =$value;
		}
		if($xinfo{"dim4"}>1){
			print "Choosing and moving files\n";
			$order = 'fslsplit '.$nii_file.' '.$output_dir.'/smc'.$subject.'s -t';
			print "$order\n";
			system($order);
		}
	}
	print "Cleaning house\n";
	$order = "rm $std{'DATA'}/tmp/*";
	system($order);
}