Hello FreeSurfer Developers,

I am running Recon1 to check/edit the Talairach and Brainmask. The process exits without error; however, I'm finding issues when I open T1.mgz and brainmask.mgz in freeview.

Chunks of putamen seem to be boxed out as white matter, but this is not evident in the other files (orig.mgz or nu.mgz). Please see the attached images.

The following is the code I am using: #007 recon-all -autorecon1 -subjid TEST007 -i [T1 file] -T2 [T2 file];

- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - Linux MSI 4.4.0-43-Microsoft #1-Microsoft Wed Dec 31 14:42:53 PST 2014 x86_64 x86_64 x86_64 GNU/Linux - Recon-all.log; see attached.

I haven't come across this error in my searches, but I may be using the wrong key terms. Would anyone be able to point me in the right direction or trouble-shoot fixing this?

Thank you for your time, Diana

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