If you happen to have another MPRAGE for this subject, sure, you can try it. Allison
On Mon, 14 May 2012, Borzello, Mia wrote: > 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.
