Hello,

My recent attempt to run recon-all on one of my MRIs was unsuccessful. I ran the command as:

recon-all -subjid ${subject} -all -time -log logfile -nuintensitycor-3T -sd $SUBJECTS_DIR -parallel

About 37 minutes into running, the process terminated with the following error:

ERROR: mri_ca_register with non-zero status 9

This is my first time using FreeSurfer, so it's very possible that I've made a mistake. However, the issue may also be that atlas-based segmentation is not a good choice for my brain. I have a magnetically-adjusted VP shunt that produces an artifact 3.5 cm in diameter on the top of my right frontal lobe of which I anticipate would make registration with a normal brain difficult.

Please let me know whether this sounds like an error in my input, in which I will be happy to produce more information, or whether I should seek an alternative solution for segmenting my brain from an MRI. Thank you!