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
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
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 [astevens@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
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 [astevens@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
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 [astevens@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 [astevens@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
would it be worth it at this point, to use another set of dicoms? thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@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 [astevens@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 [astevens@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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@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 [astevens@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 [astevens@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
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 [astevens@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 [astevens@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
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 [astevens@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 [astevens@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 [astevens@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
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 [astevens@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 [astevens@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 [astevens@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
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 [astevens@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 [astevens@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 [astevens@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
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 [fischl@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 [astevens@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 [astevens@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 [astevens@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
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 [fischl@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 [astevens@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 [astevens@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 [astevens@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
oh woops. sorry. so both of these sets of dicoms are T2 ________________________________________ From: Bruce Fischl [fischl@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 [fischl@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 [astevens@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 [astevens@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 [astevens@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
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 [fischl@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 [fischl@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 [astevens@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 [astevens@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 [astevens@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
okay, well i'll give it a try with a set of T1s. Thanks guys! ________________________________________ From: Bruce Fischl [fischl@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 [fischl@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 [fischl@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 [astevens@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 [astevens@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 [astevens@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
so that's most likely the problem? ________________________________________ From: Bruce Fischl [fischl@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 [fischl@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 [astevens@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 [astevens@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 [astevens@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@nmr.mgh.harvard.edu
-
Allison Stevens Player -
Borzello, Mia -
Bruce Fischl