[MINC-users] nu_correct directory problems

[Mishkin Derakhshan]

Hi,
I am trying to call nu_correct from perl:
ie.
#! /usr/bin/perl
chdir("/mydir/");
system("nu_correct -iter 150 -stop 5e-05 -normalize_field
file_nu_0.mnc.gz file_nu_1.mnc");


If I run this from the command line, ie.
opus[~]$ cd /mydir
opus[/mydir]$ nu_correct -iter 150 -stop 5e-05 -normalize_field
file_nu_0.mnc.gz file_nu_1.mnc

Then everything works fine.

If however, I do this:
opus[~]$ ./perlscript.pl

Then I always get the same error:
Cannot open .imp file: file_nu_1.imp
nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)

The problem seems to be that the .imp file is getting saved to the
directory I was in before I ran my perl script, and not to /mydir.

I suspect this has something to do with using chdir() in perl, and to
how nu_correct is calculating what its current directory.

Any tips?
thanks,
mishkin

opus[~]$ `which nu_correct` -version
Program nu_correct, built from:
Package MNI N3, version 1.10.1, compiled by rotor at ben
(x86_64-unknown-linux-gnu) on 2007-11-07 at 11:54:01