It also looks like you have an extra forward slash at the end of seg.mgz

On 07/02/2013 12:13 PM, Bruce Fischl wrote:

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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-seg <segmentation volume>

would be the correct flag if you wanted to specify an aseg-type volume to do the normalizaton based on instead of using a transform and the gca. You can't give it an intensity volume though (lke the nu.mgz) - it won't know what to do with it Bruce

On Tue, 2 Jul 2013, Mark Plantz wrote:

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.edu wrote: 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 atlasfrom'/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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