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 $FREESURFER_HOME/subjects/sample-001.mgz .
best, Andrew On Dec 14, 2017, at 4:00 PM, Pruett, Scott <brandon_pru...@brown.edu<mailto:brandon_pru...@brown.edu>> wrote: I just recently followed the steps to install Freesurfer on my Mac. The installation initially seems to have gone fine, but when I try to test the installation by using the listed "Example 1: Convert the sample-001.mgz to nifti format," I get the following error: -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni scott-pruetts-computer:~ scottpruett$ 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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