Hello,

I recently ran recon-all on a group of subjects with FreeSurfer 7.1.0, and for one subject some of the resulting volumes look crooked. The 001.mgz volume looks normal, but every other volume such as orig.mgz, T1.mgz, brainmask.mgz have a severe tilt to them. When we open surfaces on top of volumes, their orientations follow whichever volume is loaded first. I've attached 2 sample screenshots here. 

We suspected that this could be related to a Talairach registration issue and inspected the volumes using the following command:

tkregister2 --mgz --s $sub --fstal --surf orig

However, everything seems to be aligned correctly on here, so we're not sure if there's anything we can do. 

Is this something that needs additional correction, or can we use this data in analysis as is? I've also attached the recon-all.log in case it's helpful.

Best,

Yasemin

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