Hello, I am currently having some difficulties with the mri_ca_normalize command. I am attempting to create a normalized volume file using an input brain with the following command:
mri_ca_normalize /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/ -seg /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz/ /Applications/freesurfer/subjects/CMH-7259/mri/transforms/talairach.lta /Volumes/Wong_Lab/norm.mgz However, I am getting an error that my seg.mgz file could not be read: Operation not permitted dhcp-165-124-23-240:~ IngvalsonLab$ mri_ca_normalize /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/ -seg /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz/ /Applications/freesurfer/subjects/CMH-7259/mri/transforms/talairach.lta /Volumes/Wong_Lab/neo-atlas.gca reading 2 input volumes reading atlas from '/Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz/'... GCAread(/Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz/): could not read file Operation not permitted mri_ca_normalize: could not open GCA /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz/. I don't believe it is a permissions issue. Any ideas? Thanks, Mark
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