Hello,<br>I am trying to configure freesurfer on our Ubuntu machine so
that I can use mri_convert to convert dicom files to nifti files for
use in FSL. Our tech guy downloaded and installed it and when I typed
mri_convert in the terminal, I got the help information. However, when
I tried to actually use the command I got this:<br>
<b>$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $<br>reading from I0001.dcm...<br>--------------------------------------------------------------------------<br>ERROR: FreeSurfer environment FREESURFER_HOME is not defined.<br>





  If you are outside the NMR-Martinos Center, please set this<br>  variable to the location where you installed FreeSurfer.<br>  If you are inside the NMR-Martinos Center, please source<br>  the standard environment. If you need to install FreeSurfer,<br>





  go to: <a href="http://surfer.nmr.mgh.harvard.edu/" target="_blank">http://surfer.nmr.mgh.harvard.edu</a></b><br><br>So I looked up online how to configure freesurfer, followed the directions and got this:<br><b>-------- freesurfer-Linux-centos4-stable-pub-v4.4.0 --------<br>





Setting up environment for FreeSurfer/FS-FAST (and FSL)<br>FREESURFER_HOME   /usr/local/freesurfer<br>FSFAST_HOME       /usr/local/freesurfer/fsfast<br>FSF_OUTPUT_FORMAT nii<br>SUBJECTS_DIR      /usr/local/freesurfer/subjects<br>





MNI_DIR           /usr/local/freesurfer/mni<br></b><br>So I thought it was done correctly, but when I tried the mri_convert<br>command again, I got the same exact error.<br><br>I
thought I might have been missing the license file, but when I tried to
copy the .license text file to the /usr/local/freesurfer directory, I
got a message that there was already one there (but I don&#39;t see it when
I type ls).<br>
What am I missing or doing wrong? <br><br>Thanks,<br>


Chaleece
<br clear="all"><br>-- <br>Chaleece Sandberg, M.A.<br>Graduate Student<br>Speech Language and Hearing Sciences<br>Boston University Sargent College<br><br>