Hi Scott,

It looks like "/Users/scottpruett/sample-001.mgz" doesn’t exist because your cp command never ran (you have to specify a destination). Try:

cp $FREESURFER_HOME/subjects/sample-001.mgz .

best,

Andrew

On Dec 14, 2017, at 4:00 PM, Pruett, Scott <brandon_pruett@brown.edu> wrote:

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

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