Hey Allison, Thanks for you help. What do you mean by check your talairach? I'll hold off on using a different set of dicoms, and make that my last resort since it takes a day to complete. Thanks, m ________________________________________ From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 3:16 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] "cannot allocate memory" issue
Hi Mia, You may want to check your talairach to make sure that looks okay. If that's not causing the problem, you can edit the wm.mgz to remove the cerebellum and then rerun and this should fix the problem. Allison On Mon, 14 May 2012, Borzello, Mia wrote: > 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 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.
