We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered.

Emily

On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt <whatsdac@umich.edu> wrote:

OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed...

On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote:

> Hi Jon
>
> if you upload this subject we'll take a look
> Bruce
>
>
> On Wed, 12 Dec 2012, Jonathan Holt wrote:
>
>> I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0.
>>
>> Edited a brain and ran "recon-all -autorecon2 -autorecon3 -s subj_id" which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes.
>>
>>
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--
Emily J Rogalski, PhD
Assistant Research Professor
Northwestern University
Cognitive Neurology and Alzheimer's Disease Center (CNADC)
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Chicago, IL 60611
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.