Hi Freesurfer Team

Following up on my previous email, I have terminated the recon-all as they were was still running after 3 days. As has been noted on other threads here, I checked the wm.mgz and they all look quite bad (screenshots attached). Is this the most probable source of the XL defect? 

In xl_defect 1 and 2, should I be filling in the ventricles? 

Please let me know what I could do to save these scans! Thank you.

Best Wishes,

Shane

On 24 February 2017 at 16:21:37, Shane Schofield (shane.schofield@yahoo.com) wrote:

Hi Freesurfer Team,

I am running recon-all on Freesurfer version 6. A few of my subjects have “XL defect detected …” and their recon-all have been running for more than 20 hours. I hope this is not a silly question, but will this XL defect be corrected eventually…?

Another question, what are “defects”? Is there anything I could do to the raw T1 before recon-all?

Thanks!

Shane

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Shane Schofield