Hi all, I want to write a script which should use extern programms for MRI-preprocessing, doing several processing commands to a bunch of data. For example: running brain extraction from the command line in linux I would write bet <inputimage> <nameforoutputimage> -m Then the programm bet in fsl would be opened and skull stripping would be performed, the output image would be saved in the same folder of the inputimage. In my script I want the outputimage to be saved in an other folder. Could anyone help me with this? I think there a lot of syntax errors ... 

#!/usr/bin/perl

use strict;
use warnings;
use diagnostics;

my $dir = "usr/bin/Test_Protokoll"

my $001= "prob_001";
my $002= "prob_002";
my $003= "prob_003";

@filter: ("001", "002", "003");

#Brainextraction
foreach ("001", "002", "003")
{
   system ("bet SYNT_MPRAGE_T1_PD_B0corr YNT_MPRAGE_T1_PD_B0corr_brain
+ -m");
}

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In reply to Defining directory/Datas the perl script should work with by perlnewbie

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