You can do: tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
When you downloaded FreeSurfer, you would have also received the subject "bert" who is a good example to compare to. He will likely be located in: $FREESURFER_HOME/subjects/bert If you do the same command above for bert: tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix You'll see what the filled.mgz should look like. Allison On Mon, 14 May 2012, Borzello, Mia wrote: > How do I check this? (Apologies for my ignorance.) So I might need to just > use a different set of dicoms then? > > thanks, > Mia > ________________________________________ > From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] > Sent: Monday, May 14, 2012 1:02 PM > To: Borzello, Mia > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] "cannot allocate memory" issue > > It looks like there is too huge a topology error for it to continue: > > CORRECTING DEFECT 23 (vertices=143258, convex hull=19937) > Excessive topologic defect encountered: could not allocate -729782272 > edges for retessellation > Cannot allocate memory > > I would suggested looking at the filled.mgz to make sure skull and/or > cerebellum are not included. > Allison > > On Mon, 14 May 2012, Borzello, Mia wrote: > >> Hi all, >> >> I was wondering if you could help me figure out why the recon isn't running >> to completion. I've attached the log file (recon-all.log), but it's unclear >> to me what I should do to fix this problem. I tried to compute the lh.pial, >> but I guess it was never made in the recon. >> >> Thanks so much, >> Mia >> > > > _______________________________________________ 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.
