It is hard to say from those pics what is wrong as you need to look at the ?h.orig.nofix surface on the scans. It looks like there is a lot of skull left there, so it may be that the surface is extending out to the skull. I don't think it is a problem with the ventricles.

On 2/26/17 6:58 AM, Shane Schofield wrote:

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 mailto: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

-- Shane Schofield

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Thanks Doug, I will give it try and update you on it.

S

--  Shane Schofield

On 26 February 2017 at 22:35:52, Douglas Greve (greve@nmr.mgh.harvard.edu) wrote:

Probably not. Probably you the cerebellum is still attached. You should check the wm.mgz volume.

On 2/24/17 11:21 AM, Shane Schofield 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

--  Shane Schofield

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