Hi Mark

for mri_ca_normalize all the optional arguments (prefixed with a dash) must come before all the mandatory ones. Also, you shouldn't give it the mri directory - give it an input volume (like nu.mgz).

cheers
Bruce

On Tue, 2 Jul 2013, Mark Plantz wrote:

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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