Hello everybody,
I have a problem running make_average_subject for a large number of subjects (>400) on a Mac Intel. I tried with different Freesurfer versions (all the log outputs are attached). Using the freesurfer version 4.3 and 4.4 the make_average_subject script always stop at the 297th subject with the error "Cannot allocate memory". I already tried to uncomment the line "limit descriptors unlimited" or to set it to various values, as proposed in the mailing list, but without success (it always stop at the 297th subject). Then I tried with the Freesurfer version 4.5 (therefore I had to recompute the lh.inflated.H and lh.inflated.K which are not automatically produced in previous versions), but with the 4.5 version I got a strange "license error" message in the middle of the script (and my licence is certainly fine as I can run any other script without problems).
Does anyone have an idea? Many thanks in advance for your precious help,
Marie
try adding --no-aseg to the command line. that out-of-memory error seems to originate with creation of the average aseg.mgz file (hopefully you wont need it for your subject set, typically you dont need aseg.mgz since aseg stats are usually gathered from a set of aseg.stats files, not from an average aseg.mgz).
doug: maybe we should make --no-aseg the default?
n.
On Fri, 2010-05-28 at 21:31 +0200, Marie Schaer wrote:
Hello everybody,
I have a problem running make_average_subject for a large number of subjects (>400) on a Mac Intel. I tried with different Freesurfer versions (all the log outputs are attached). Using the freesurfer version 4.3 and 4.4 the make_average_subject script always stop at the 297th subject with the error "Cannot allocate memory". I already tried to uncomment the line "limit descriptors unlimited" or to set it to various values, as proposed in the mailing list, but without success (it always stop at the 297th subject). Then I tried with the Freesurfer version 4.5 (therefore I had to recompute the lh.inflated.H and lh.inflated.K which are not automatically produced in previous versions), but with the 4.5 version I got a strange "license error" message in the middle of the script (and my licence is certainly fine as I can run any other script without problems).
Does anyone have an idea? Many thanks in advance for your precious help,
Marie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
Thank you very much for your rapid response. I tried with make_average_subject --no-aseg, but --no-aseg seems to be an option for make_average_volume (?). Do I need to run make_average_volume first and then make_average_surface?
Thank you very much,
Marie
On 28 mai 10, at 21:37, Nick Schmansky wrote:
try adding --no-aseg to the command line. that out-of-memory error seems to originate with creation of the average aseg.mgz file (hopefully you wont need it for your subject set, typically you dont need aseg.mgz since aseg stats are usually gathered from a set of aseg.stats files, not from an average aseg.mgz).
doug: maybe we should make --no-aseg the default?
n.
On Fri, 2010-05-28 at 21:31 +0200, Marie Schaer wrote:
Hello everybody,
I have a problem running make_average_subject for a large number of subjects (>400) on a Mac Intel. I tried with different Freesurfer versions (all the log outputs are attached). Using the freesurfer version 4.3 and 4.4 the make_average_subject script always stop at the 297th subject with the error "Cannot allocate memory". I already tried to uncomment the line "limit descriptors unlimited" or to set it to various values, as proposed in the mailing list, but without success (it always stop at the 297th subject). Then I tried with the Freesurfer version 4.5 (therefore I had to recompute the lh.inflated.H and lh.inflated.K which are not automatically produced in previous versions), but with the 4.5 version I got a strange "license error" message in the middle of the script (and my licence is certainly fine as I can run any other script without problems).
Does anyone have an idea? Many thanks in advance for your precious help,
Marie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, i think you will need to run them separately (make_average_subject is just a wrapper that calls make_average_volume then make_average_surface).
n.
On Fri, 2010-05-28 at 22:12 +0200, Marie Schaer wrote:
Hi Nick,
Thank you very much for your rapid response. I tried with make_average_subject --no-aseg, but --no-aseg seems to be an option for make_average_volume (?). Do I need to run make_average_volume first and then make_average_surface?
Thank you very much,
Marie
On 28 mai 10, at 21:37, Nick Schmansky wrote:
try adding --no-aseg to the command line. that out-of-memory error seems to originate with creation of the average aseg.mgz file (hopefully you wont need it for your subject set, typically you dont need aseg.mgz since aseg stats are usually gathered from a set of aseg.stats files, not from an average aseg.mgz).
doug: maybe we should make --no-aseg the default?
n.
On Fri, 2010-05-28 at 21:31 +0200, Marie Schaer wrote:
Hello everybody,
I have a problem running make_average_subject for a large number of subjects (>400) on a Mac Intel. I tried with different Freesurfer versions (all the log outputs are attached). Using the freesurfer version 4.3 and 4.4 the make_average_subject script always stop at the 297th subject with the error "Cannot allocate memory". I already tried to uncomment the line "limit descriptors unlimited" or to set it to various values, as proposed in the mailing list, but without success (it always stop at the 297th subject). Then I tried with the Freesurfer version 4.5 (therefore I had to recompute the lh.inflated.H and lh.inflated.K which are not automatically produced in previous versions), but with the 4.5 version I got a strange "license error" message in the middle of the script (and my licence is certainly fine as I can run any other script without problems).
Does anyone have an idea? Many thanks in advance for your precious help,
Marie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
Sorry for disturbing again. As advised, I tried to launch separately make_average_volume and make_average_surface. Even with the --no-aseg option with make_average_volume I got the "cannot allocate memory" error. And with the make_average_surface I got the "license error" in the middle of one subject processing... Any idea?
Thank you very much,
Marie
On 28 mai 10, at 21:37, Nick Schmansky wrote:
try adding --no-aseg to the command line. that out-of-memory error seems to originate with creation of the average aseg.mgz file (hopefully you wont need it for your subject set, typically you dont need aseg.mgz since aseg stats are usually gathered from a set of aseg.stats files, not from an average aseg.mgz).
doug: maybe we should make --no-aseg the default?
n.
On Fri, 2010-05-28 at 21:31 +0200, Marie Schaer wrote:
Hello everybody,
I have a problem running make_average_subject for a large number of subjects (>400) on a Mac Intel. I tried with different Freesurfer versions (all the log outputs are attached). Using the freesurfer version 4.3 and 4.4 the make_average_subject script always stop at the 297th subject with the error "Cannot allocate memory". I already tried to uncomment the line "limit descriptors unlimited" or to set it to various values, as proposed in the mailing list, but without success (it always stop at the 297th subject). Then I tried with the Freesurfer version 4.5 (therefore I had to recompute the lh.inflated.H and lh.inflated.K which are not automatically produced in previous versions), but with the 4.5 version I got a strange "license error" message in the middle of the script (and my licence is certainly fine as I can run any other script without problems).
Does anyone have an idea? Many thanks in advance for your precious help,
Marie
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.
Hi everyone,
I did not find a solution to my problem yet: how to launch make_average_subject / make_average_volume / make_average_surface on a large number of subjects on a Mac Intel? Did someone encounter this error before?
Many thanks in advance for your help,
Marie
On 29 mai 10, at 20:07, Marie Schaer wrote:
Hi Nick,
Sorry for disturbing again. As advised, I tried to launch separately make_average_volume and make_average_surface. Even with the --no-aseg option with make_average_volume I got the "cannot allocate memory" error. And with the make_average_surface I got the "license error" in the middle of one subject processing... Any idea?
Thank you very much,
Marie
On 28 mai 10, at 21:37, Nick Schmansky wrote:
try adding --no-aseg to the command line. that out-of-memory error seems to originate with creation of the average aseg.mgz file (hopefully you wont need it for your subject set, typically you dont need aseg.mgz since aseg stats are usually gathered from a set of aseg.stats files, not from an average aseg.mgz).
doug: maybe we should make --no-aseg the default?
n.
On Fri, 2010-05-28 at 21:31 +0200, Marie Schaer wrote:
Hello everybody,
I have a problem running make_average_subject for a large number of subjects (>400) on a Mac Intel. I tried with different Freesurfer versions (all the log outputs are attached). Using the freesurfer version 4.3 and 4.4 the make_average_subject script always stop at the 297th subject with the error "Cannot allocate memory". I already tried to uncomment the line "limit descriptors unlimited" or to set it to various values, as proposed in the mailing list, but without success (it always stop at the 297th subject). Then I tried with the Freesurfer version 4.5 (therefore I had to recompute the lh.inflated.H and lh.inflated.K which are not automatically produced in previous versions), but with the 4.5 version I got a strange "license error" message in the middle of the script (and my licence is certainly fine as I can run any other script without problems).
Does anyone have an idea? Many thanks in advance for your precious help,
Marie
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Marie,
how much ram do you have? Most people are off to Heidelberg to teach the FS(L) course, so it may be a bit before you hear from anyone.
Bruce
On Mon, 31 May 2010, Marie Schaer wrote:
Hi everyone,
I did not find a solution to my problem yet: how to launch make_average_subject / make_average_volume / make_average_surface on a large number of subjects on a Mac Intel? Did someone encounter this error before?
Many thanks in advance for your help,
Marie
On 29 mai 10, at 20:07, Marie Schaer wrote:
Hi Nick,
Sorry for disturbing again. As advised, I tried to launch separately make_average_volume and make_average_surface. Even with the --no-aseg option with make_average_volume I got the "cannot allocate memory" error. And with the make_average_surface I got the "license error" in the middle of one subject processing... Any idea?
Thank you very much,
Marie
On 28 mai 10, at 21:37, Nick Schmansky wrote:
try adding --no-aseg to the command line. that out-of-memory error seems to originate with creation of the average aseg.mgz file (hopefully you wont need it for your subject set, typically you dont need aseg.mgz since aseg stats are usually gathered from a set of aseg.stats files, not from an average aseg.mgz).
doug: maybe we should make --no-aseg the default?
n.
On Fri, 2010-05-28 at 21:31 +0200, Marie Schaer wrote:
Hello everybody,
I have a problem running make_average_subject for a large number of subjects (>400) on a Mac Intel. I tried with different Freesurfer versions (all the log outputs are attached). Using the freesurfer version 4.3 and 4.4 the make_average_subject script always stop at the 297th subject with the error "Cannot allocate memory". I already tried to uncomment the line "limit descriptors unlimited" or to set it to various values, as proposed in the mailing list, but without success (it always stop at the 297th subject). Then I tried with the Freesurfer version 4.5 (therefore I had to recompute the lh.inflated.H and lh.inflated.K which are not automatically produced in previous versions), but with the 4.5 version I got a strange "license error" message in the middle of the script (and my licence is certainly fine as I can run any other script without problems).
Does anyone have an idea? Many thanks in advance for your precious help,
Marie
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.
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
can you try adding the flag --debug to make_average_volume? it will output a lot of stuff, but will pinpoint at which stage it is running out of memory. also, try running 'top' in another terminal to monitor the amount of memory it's consuming while running.
as for the license error, that is bizarre, i can't think of a reason for that, unless your subjects are located on an NFS drive (a network). we've seen lots of problems with NFS and the Mac OS, where the connection drops for a couple seconds.
n.
On Mon, 2010-05-31 at 22:39 +0200, Marie Schaer wrote:
Hi everyone,
I did not find a solution to my problem yet: how to launch make_average_subject / make_average_volume / make_average_surface on a large number of subjects on a Mac Intel? Did someone encounter this error before?
Many thanks in advance for your help,
Marie
On 29 mai 10, at 20:07, Marie Schaer wrote:
Hi Nick,
Sorry for disturbing again. As advised, I tried to launch separately make_average_volume and make_average_surface. Even with the --no-aseg option with make_average_volume I got the "cannot allocate memory" error. And with the make_average_surface I got the "license error" in the middle of one subject processing... Any idea?
Thank you very much,
Marie
On 28 mai 10, at 21:37, Nick Schmansky wrote:
try adding --no-aseg to the command line. that out-of-memory error seems to originate with creation of the average aseg.mgz file (hopefully you wont need it for your subject set, typically you dont need aseg.mgz since aseg stats are usually gathered from a set of aseg.stats files, not from an average aseg.mgz).
doug: maybe we should make --no-aseg the default?
n.
On Fri, 2010-05-28 at 21:31 +0200, Marie Schaer wrote:
Hello everybody,
I have a problem running make_average_subject for a large number of subjects (>400) on a Mac Intel. I tried with different Freesurfer versions (all the log outputs are attached). Using the freesurfer version 4.3 and 4.4 the make_average_subject script always stop at the 297th subject with the error "Cannot allocate memory". I already tried to uncomment the line "limit descriptors unlimited" or to set it to various values, as proposed in the mailing list, but without success (it always stop at the 297th subject). Then I tried with the Freesurfer version 4.5 (therefore I had to recompute the lh.inflated.H and lh.inflated.K which are not automatically produced in previous versions), but with the 4.5 version I got a strange "license error" message in the middle of the script (and my licence is certainly fine as I can run any other script without problems).
Does anyone have an idea? Many thanks in advance for your precious help,
Marie
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Marie Schaer -
Nick Schmansky