Re: [Freesurfer] "cannot allocate memory" issue
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 >>>>>
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 2
Re: [Freesurfer] "cannot allocate memory" issue
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
Re: [Freesurfer] "cannot allocate memory" issue
so that's most likely the problem? 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 >>>&g
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.
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.
Re: [Freesurfer] "cannot allocate memory" issue
There are instructions on how to check it here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach 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 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.
Re: [Freesurfer] "cannot allocate memory" issue
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.
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.
Re: [Freesurfer] "cannot allocate memory" issue
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.
Re: [Freesurfer] "cannot allocate memory" issue
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.
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 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.
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.
Re: [Freesurfer] "cannot allocate memory" issue
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.
