Hi Mia can you clarify what you mean by "a different set of dicoms"? Did you acquire more than 1 T1-weighted structural on this subject? And can you send us an image of the acquisition, say in coronal view?
thanks Bruce On Mon, 14 May 2012, Borzello, Mia wrote: > 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 > > > _______________________________________________ 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.
