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 <whats...@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. > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogal...@gmail.com
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