oh woops. sorry. so both of these sets of dicoms are T2 ________________________________________ From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 3:46 PM To: Borzello, Mia Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] "cannot allocate memory" issue
actually I wanted one from tkmedit. Can you tell us something about the acquisition? What kind of scan is it? What resolution? And if you can send us images from tkmedit in coronal and sagittal view that would help too (say of the orig.mgz) Bruce On Mon, 14 May 2012, Borzello, Mia wrote: > I have two sets of dicoms: one is an axial view, while the other is coronal > (this is the one i was using). I attached a screenshot. I'm not sure if > that's what you wanted? > > thanks > mia > ________________________________________ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Monday, May 14, 2012 3:32 PM > To: Borzello, Mia > Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] "cannot allocate memory" issue > > 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.
