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