#!/usr/bin/perl
use strict;
use warnings;
use File::Find::Rule;
use File::Path qw(make_path);
use Data::Dump qw(dump);
my $idir = '/old_nas/adni/ADNI';
my $odir = '/nas/data/gadni/bids';
my $rules = '/nas/data/gadni/gadni_mri.csv';

my %subjects;
open IRF, "<$rules" or die "\nNo rules file\n\n";
while (<IRF>){
	my ($skey, $svalue) = /(\d{4});(.*)/;
	$subjects{$skey} = $svalue;
}
#dump %subjects; 
foreach my $subject (sort keys %subjects){
	my $opath = $odir.'/sub-'.$subject.'/anat';
	make_path($opath) unless (-d $opath);
	my $ipath = $idir.'/'.$subjects{$subject};
	my @niftis = find(file => 'name' => '*.nii', in => $ipath);
	my $count = 1;
	foreach my $isrc (@niftis){
		my $itrg = $opath.'/sub-'.$subject.'_run-'.sprintf("%02d", $count).'_T1w.nii.gz';
		my $order = 'mri_convert --conform '.$isrc.' '.$itrg;
		print "$order\n";
		system($order);
		$count++;
	}
}