External Email - Use Caution
Dear experts,
while running one of my subjects, I got this error:
MRISalloc(732595, 480): could not allocate vertices
Cannot allocate memory
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019
Do you know what went wrong and how I can fix this?
Best regards,
Julia
Hi Julia
can you send us the recon-all.log file?
cheers Bruce On Tue, 12 Feb 2019, Julia Ströhlein wrote:
External Email - Use Caution
Dear experts,
while running one of my subjects, I got this error:
MRISalloc(732595, 480): could not allocate vertices
Cannot allocate memory
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019
Do you know what went wrong and how I can fix this?
Best regards,
Julia
Unbenannt
External Email - Use Caution
Hi, of course.
Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Februar 2019 16:12 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
can you send us the recon-all.log file?
cheers Bruce On Tue, 12 Feb 2019, Julia Ströhlein wrote:
External Email - Use Caution
Dear experts,
while running one of my subjects, I got this error:
MRISalloc(732595, 480): could not allocate vertices
Cannot allocate memory
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019
Do you know what went wrong and how I can fix this?
Best regards,
Julia
Unbenannt
Hi Julia
I think you only have about 1.5G free memory at the beinning of running recon-all, which is not enough for this subject. It looks like some other process is using another 2G, which might be enough if you can free it up. In general though you probably want a machine with more ram
cheers Bruce
On Wed, 13 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi, of course.
Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Februar 2019 16:12 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
can you send us the recon-all.log file?
cheers Bruce On Tue, 12 Feb 2019, Julia Ströhlein wrote:
External Email - Use Caution
Dear experts,
while running one of my subjects, I got this error:
MRISalloc(732595, 480): could not allocate vertices
Cannot allocate memory
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019
Do you know what went wrong and how I can fix this?
Best regards,
Julia
Unbenannt
External Email - Use Caution
Hi Bruce, thanks for the advice. I ran the subject again with 4.5G, but it ended with the same error. It only happens with this subject, the stream worked fine for all the other subjects. However, I tried running the subject with my Macbook, and it also ended with an error (see the recon-all.log attached). I think it has something to do with the MRI of the subject. Do you have any ideas? Thanks for any help. Best, Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Mittwoch, 13. Februar 2019 15:58 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
I think you only have about 1.5G free memory at the beinning of running recon-all, which is not enough for this subject. It looks like some other process is using another 2G, which might be enough if you can free it up. In general though you probably want a machine with more ram
cheers Bruce
On Wed, 13 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi, of course.
Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Februar 2019 16:12 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
can you send us the recon-all.log file?
cheers Bruce On Tue, 12 Feb 2019, Julia Ströhlein wrote:
External Email - Use Caution
Dear experts,
while running one of my subjects, I got this error:
MRISalloc(732595, 480): could not allocate vertices
Cannot allocate memory
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019
Do you know what went wrong and how I can fix this?
Best regards,
Julia
Unbenannt
Hi Julia
why don't you tar and gzip the subject directory and put it on our ftp site so we can take a look
cheers Bruce On Mon, 18 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi Bruce, thanks for the advice. I ran the subject again with 4.5G, but it ended with the same error. It only happens with this subject, the stream worked fine for all the other subjects. However, I tried running the subject with my Macbook, and it also ended with an error (see the recon-all.log attached). I think it has something to do with the MRI of the subject. Do you have any ideas? Thanks for any help. Best, Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Mittwoch, 13. Februar 2019 15:58 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
I think you only have about 1.5G free memory at the beinning of running recon-all, which is not enough for this subject. It looks like some other process is using another 2G, which might be enough if you can free it up. In general though you probably want a machine with more ram
cheers Bruce
On Wed, 13 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi, of course.
Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Februar 2019 16:12 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
can you send us the recon-all.log file?
cheers Bruce On Tue, 12 Feb 2019, Julia Ströhlein wrote:
External Email - Use Caution
Dear experts,
while running one of my subjects, I got this error:
MRISalloc(732595, 480): could not allocate vertices
Cannot allocate memory
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019
Do you know what went wrong and how I can fix this?
Best regards,
Julia
Unbenannt
External Email - Use Caution
Hi Bruce,
I created a link with the Martinos File Drop System, because ftp upload did not work. It's probably the best idea to send the links to your personal mail address?
Best Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Montag, 18. Februar 2019 15:52 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
why don't you tar and gzip the subject directory and put it on our ftp site so we can take a look
cheers Bruce On Mon, 18 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi Bruce, thanks for the advice. I ran the subject again with 4.5G, but it ended with the same error. It only happens with this subject, the stream worked fine for all the other subjects. However, I tried running the subject with my Macbook, and it also ended with an error (see the recon-all.log attached). I think it has something to do with the MRI of the subject. Do you have any ideas? Thanks for any help. Best, Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Mittwoch, 13. Februar 2019 15:58 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
I think you only have about 1.5G free memory at the beinning of running recon-all, which is not enough for this subject. It looks like some other process is using another 2G, which might be enough if you can free it up. In general though you probably want a machine with more ram
cheers Bruce
On Wed, 13 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi, of course.
Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Februar 2019 16:12 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
can you send us the recon-all.log file?
cheers Bruce On Tue, 12 Feb 2019, Julia Ströhlein wrote:
External Email - Use Caution
Dear experts,
while running one of my subjects, I got this error:
MRISalloc(732595, 480): could not allocate vertices
Cannot allocate memory
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019
Do you know what went wrong and how I can fix this?
Best regards,
Julia
Unbenannt
Hi Julia
did you upload the entire subject dir (gzipped and tarred)? And what happened with ftp? We can help you get that working. I would think the whole subject dir would be too big for the filedrop, but feel free to send me the link
cheers Bruce On Tue, 19 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi Bruce,
I created a link with the Martinos File Drop System, because ftp upload did not work. It's probably the best idea to send the links to your personal mail address?
Best Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Montag, 18. Februar 2019 15:52 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
why don't you tar and gzip the subject directory and put it on our ftp site so we can take a look
cheers Bruce On Mon, 18 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi Bruce, thanks for the advice. I ran the subject again with 4.5G, but it ended with the same error. It only happens with this subject, the stream worked fine for all the other subjects. However, I tried running the subject with my Macbook, and it also ended with an error (see the recon-all.log attached). I think it has something to do with the MRI of the subject. Do you have any ideas? Thanks for any help. Best, Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Mittwoch, 13. Februar 2019 15:58 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
I think you only have about 1.5G free memory at the beinning of running recon-all, which is not enough for this subject. It looks like some other process is using another 2G, which might be enough if you can free it up. In general though you probably want a machine with more ram
cheers Bruce
On Wed, 13 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi, of course.
Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Februar 2019 16:12 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
can you send us the recon-all.log file?
cheers Bruce On Tue, 12 Feb 2019, Julia Ströhlein wrote:
External Email - Use Caution
Dear experts,
while running one of my subjects, I got this error:
MRISalloc(732595, 480): could not allocate vertices
Cannot allocate memory
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019
Do you know what went wrong and how I can fix this?
Best regards,
Julia
Unbenannt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce, did you receive the link I sent you last week? Best Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 19. Februar 2019 16:37 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
did you upload the entire subject dir (gzipped and tarred)? And what happened with ftp? We can help you get that working. I would think the whole subject dir would be too big for the filedrop, but feel free to send me the link
cheers Bruce On Tue, 19 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi Bruce,
I created a link with the Martinos File Drop System, because ftp upload did not work. It's probably the best idea to send the links to your personal mail
address?
Best Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Montag, 18. Februar 2019 15:52 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
why don't you tar and gzip the subject directory and put it on our ftp site so we can take a look
cheers Bruce On Mon, 18 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi Bruce, thanks for the advice. I ran the subject again with 4.5G, but it ended with the same error. It only happens with this subject, the stream worked fine for all the other subjects. However, I tried running the subject with my Macbook, and it also ended with an error (see the recon-all.log attached). I think it has something to do with the MRI of the subject. Do you have any ideas? Thanks for any help. Best, Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Mittwoch, 13. Februar 2019 15:58 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
I think you only have about 1.5G free memory at the beinning of running recon-all, which is not enough for this subject. It looks like some other process is using another 2G, which might be enough if you can free it up. In general though you probably want a machine with more ram
cheers Bruce
On Wed, 13 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi, of course.
Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Februar 2019 16:12 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
can you send us the recon-all.log file?
cheers Bruce On Tue, 12 Feb 2019, Julia Ströhlein wrote:
External Email - Use Caution
Dear experts,
while running one of my subjects, I got this error:
MRISalloc(732595, 480): could not allocate vertices
Cannot allocate memory
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019
Do you know what went wrong and how I can fix this?
Best regards,
Julia
Unbenannt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Julia,
I've taken a look at the data you sent us last week and it looks like the issue is stemming from the topology fixer. If you look through the input scan you've given us, you can see that the contrast between wm/gm is especially low in certain regions. This low contrast to noise ratio is making it hard for recon-all to produce a good wm segmentation which in turn gives the topology fixer trouble "cleaning up" the surfaces. This is causing your memory allocation error.
You may be able to improve the segmentation by including an expert.opts file with mri_segment adjustments (-wlo flag). Check out our resources on expert.opts files and the mri_segment option bellow:
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segment
I hope this helps.
Best, Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Julia Ströhlein stroehlein@sportmed.uni-paderborn.de Sent: Tuesday, February 26, 2019 1:54 AM To: 'Freesurfer support list' Subject: Re: [Freesurfer] MRISalloc error during automatic reconstruction
External Email - Use Caution
Hi Bruce, did you receive the link I sent you last week? Best Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 19. Februar 2019 16:37 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
did you upload the entire subject dir (gzipped and tarred)? And what happened with ftp? We can help you get that working. I would think the whole subject dir would be too big for the filedrop, but feel free to send me the link
cheers Bruce On Tue, 19 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi Bruce,
I created a link with the Martinos File Drop System, because ftp upload did not work. It's probably the best idea to send the links to your personal mail
address?
Best Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Montag, 18. Februar 2019 15:52 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
why don't you tar and gzip the subject directory and put it on our ftp site so we can take a look
cheers Bruce On Mon, 18 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi Bruce, thanks for the advice. I ran the subject again with 4.5G, but it ended with the same error. It only happens with this subject, the stream worked fine for all the other subjects. However, I tried running the subject with my Macbook, and it also ended with an error (see the recon-all.log attached). I think it has something to do with the MRI of the subject. Do you have any ideas? Thanks for any help. Best, Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Mittwoch, 13. Februar 2019 15:58 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
I think you only have about 1.5G free memory at the beinning of running recon-all, which is not enough for this subject. It looks like some other process is using another 2G, which might be enough if you can free it up. In general though you probably want a machine with more ram
cheers Bruce
On Wed, 13 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionHi, of course.
Julia
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Februar 2019 16:12 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction
Hi Julia
can you send us the recon-all.log file?
cheers Bruce On Tue, 12 Feb 2019, Julia Ströhlein wrote:
External Email - Use CautionDear experts,
while running one of my subjects, I got this error:
MRISalloc(732595, 480): could not allocate vertices
Cannot allocate memory
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST 2019
Do you know what went wrong and how I can fix this?
Best regards,
Julia
Unbenannt
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Diamond, Bram Ryder -
Julia Ströhlein