Hi Chaleece,
you need to define the FREESURFER_HOME environment variable. For example:
setenv FREESURFER_HOME /usr/local/freesurfer
cheers, Bruce
On Mon, 12 Oct 2009, Chaleece Sandberg wrote:
Hello, 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: *$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I0001.dcm...
ERROR: FreeSurfer environment FREESURFER_HOME is not defined. If you are outside the NMR-Martinos Center, please set this variable to the location where you installed FreeSurfer. If you are inside the NMR-Martinos Center, please source the standard environment. If you need to install FreeSurfer, go to: http://surfer.nmr.mgh.harvard.edu*
So I looked up online how to configure freesurfer, followed the directions and got this: *-------- freesurfer-Linux-centos4-stable-pub-v4.4.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni
So I thought it was done correctly, but when I tried the mri_convert command again, I got the same exact error.
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't see it when I type ls). What am I missing or doing wrong?
Thanks, Chaleece