#!/usr/bin/perl -w
use strict;
use warnings;
use Data::Dump qw(dump);
my $frules = "rids.csv";
my $adni_s = "ADNI";
my $dest = "mri";
my $series = 0;
my %arules;
open IDR, "<$frules" or die "No rules file here, asshole\n";
while(<IDR>){
	if(/^\d{4},.*/){
		my ($value, $key) = /^(\d*),(.*)$/;
		chomp $key;
		$arules{$key} = $value;
	}
}
close(IDR);
foreach my $ptid (sort keys %arules){
	if(-d "$adni_s/$ptid"){
		my $ford = 'find '.$adni_s.'/'.$ptid.'/ -name *.nii';
		my @s_files = qx/$ford/;
		my $count = 10;
		foreach my $nii_file (@s_files){
			chomp $nii_file;
			$count++;
			my $wn = sprintf("%04d", $count);
			my $order = "\$FSLDIR/bin/imcp $nii_file $dest/smc$arules{$ptid}s$wn.nii.gz";
			system($order);	
		}
	}
}