Can you load the volume from menu File -> Load Volume? Ruopeng
On Feb 2, 2023, at 2:21 PM, Lauren Stephens <laure...@stanford.edu<mailto:laure...@stanford.edu>> wrote: External Email - Use Caution Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laure...@stanford.edu<mailto:laure...@stanford.edu> P: (650)-725-1716 ________________________________ From: Lauren Stephens Sent: Thursday, February 2, 2023 11:18 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto: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: laure...@stanford.edu<mailto:laure...@stanford.edu> P: (650)-725-1716 <Screenshot 2023-02-02 at 10.53.55 AM.png><Screenshot 2023-02-02 at 10.54.52 AM.png>_______________________________________________ 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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