I just recently followed the steps to install Freesurfer on my Mac. The installation initially seems to have gone fine, but when I try to test the installation by using the listed "Example 1: Convert the sample-001.mgz to nifti format,"
I get the following error:
-------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME
/Applications/freesurfer
FSFAST_HOME
/Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR
/Applications/freesurfer/subjects
MNI_DIR
/Applications/freesurfer/mni
scott-pruetts-computer:~ scottpruett$ cp $FREESURFER_HOME/subjects/sample-001.mgz
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory
scott-pruetts-computer:~ scottpruett$ mri_convert sample-001.mgz sample-001.nii.gz
mri_convert.bin sample-001.mgz sample-001.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from sample-001.mgz...
mghRead(/Users/scottpruett/sample-001.mgz, -1): could not open file
scott-pruetts-computer:~ scottpruett$
Any ideas about what I should do to remedy this?
Thanks,
Scott
--
Scott Pruett, M.D., Ph.D.
General Psychiatry and R25 Research Track Resident, PGY4
Department of Psychiatry and Human Behavior
Warren Alpert Medical School of Brown University