would it be worth it at this point, to use another set of dicoms? thanks, m ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, May 14, 2012 1:37 PM To: Allison Stevens Player Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] "cannot allocate memory" issue
It says that it couldn't open rh.orig.nofix and lh.orig.nofix. On the popup image, it doesn't look like the skull is present, but it does look like the cerebellum is. ________________________________________ From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 1:28 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] "cannot allocate memory" issue 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 _______________________________________________ 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.
