okay, well i'll give it a try with a set of T1s. Thanks guys! ________________________________________ From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 3:57 PM To: Borzello, Mia Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] "cannot allocate memory" issue
yes, that's the kind of thing I was worried about. You need a relatively high resolution set of T1s (mprage, FLASH/SPGR, close to 1mm isotropic). On Mon, 14 May 2012, Borzello, Mia wrote: > 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.
