Hi Bruce,
Is -seg the correct flag to input an .mgz file instead of a .gca atlas? After making the recommened changes, the command will not seem to work. My input is as follows:
mri_ca_normalize -seg /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-7549/mri/nu.mgz /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
Thanks for all the help
- Mark
On Tue, Jul 2, 2013 at 11:13 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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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