External Email - Use Caution
Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laurenss@stanford.edu
P: (650)-725-1716
________________________________ From: Lauren Stephens Sent: Thursday, February 2, 2023 11:18 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Error:mghRead
Hi Freesurfer Developers,
I am attempting to open a NIFTI file in freeview. Freeview will open however, it gives the error "Failed to load MRI" and then the location and name of the file. We did verify that the nifti file does open regularly when accessed on the desktop. Below is the code used and the error in the terminal. What suggestions do you have to get the file to open in freeview?
Last login: Tue Jan 31 13:34:25 on ttys001
-bash: $: command not found
-------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer/7.1.1
FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects
MNI_DIR /Applications/freesurfer/7.1.1/mni
FSL_DIR /usr/local/fsl
PSYC-C02DP05D0833:~ corpuscallosum$ cd Desktop/freesurfer_qc
PSYC-C02DP05D0833:freesurfer_qc corpuscallosum$ freeview -v \
CS040/mri/brainmask.mgz \
CS040/mri/wm.mgz:visible=0 \
CS040/mri/orig.mgz:visible=0 \
CS040/mri/aparc.a2009s+aseg.mgz:visible=0 \
-f CS040/surf/lh.white:edgecolor=yellow \
CS040/surf/rh.white:edgecolor=yellow \
CS040/surf/rh.pial:edgecolor=red \
CS040/surf/lh.pial:edgecolor=red \
-viewport cor -layout 4
error: mghRead(/Users/corpuscallosum/Desktop/freesurfer_qc/CS040/mri/brainmask.mgz, -1): could not open file
MRIread failed: Unable to read from /Users/corpuscallosum/Desktop/freesurfer_qc/CS040/mri/brainmask.mgz
PSYC-C02DP05D0833:freesurfer_qc corpuscallosum$
We are using a Mac on Ventura 13.2, Terminal Version 2.13. Freesurfer version 7.1.1.
Thank you,
Lauren Stephens
Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laurenss@stanford.edu
P: (650)-725-1716
