Re: [Freesurfer] make average subject error
it sounds like you ran out of memory. How much RAM do you have on your machine? On Tue, 14 Feb 2012, Adam David Felton wrote: Hello, I have run into an error while trying to make an average subject using 200 scans. When I ran this command I got an error: make_average_subject --xform talairach.xfm --out 200avgsub --subjects The error: Allocing output mri_concat(40491) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13726th slice Cannot allocate memory WARNING: could not create average segmentation for aseg ... ... but continuing make_average_volume done The average sub folder does not contain aseg.mgz and p.aseg.mgz files. The version of Freesurfer I am using: v 1.313.2.6 2010/08/04 15:50:56 nicks My memory: 8 GB 1333 MHz DDR3 Hard-drive: 276.49 GB free MAC OS X v 10.6.8 I have scoured the archives for the answer to my question to no avail. All of the answers before seemed to revolve around versions of Freesurfer which I expect were updated. Nick Schmanksy wrote sorry, i meant to say include the --no-aseg flag with make_average_volume (make_average_subject is just a wrapper script that calls make_average_volume and make_average_surface). But wouldn't this prevent segmentation? Is there a way to then add segmentation after? Sorry if these are novice questions (as I am a novice). Thank you, Adam ___ 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] make average subject error
Try running it with --no-aseg. doug Adam David Felton wrote: Hello, I have run into an error while trying to make an average subject using 200 scans. When I ran this command I got an error: *make_average_subject --xform talairach.xfm --out 200avgsub --subjects* The error: Allocing output mri_concat(40491) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13726th slice Cannot allocate memory WARNING: could not create average segmentation for aseg ... ... but continuing make_average_volume done The average sub folder does not contain aseg.mgz and p.aseg.mgz files. *The version of Freesurfer I am using:* v 1.313.2.6 2010/08/04 15:50:56 nicks *My memory:* 8 GB 1333 MHz DDR3 *Hard-drive:* 276.49 GB free MAC OS X v 10.6.8 I have scoured the archives for the answer to my question to no avail. All of the answers before seemed to revolve around versions of Freesurfer which I expect were updated. Nick Schmanksy wrote sorry, i meant to say include the --no-aseg flag with make_average_volume (make_average_subject is just a wrapper script that calls make_average_volume and make_average_surface). But wouldn't this prevent segmentation? Is there a way to then add segmentation after? Sorry if these are novice questions (as I am a novice). Thank you, Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] make average subject error
Hello, I have run into an error while trying to make an average subject using 200 scans. When I ran this command I got an error: *make_average_subject --xform talairach.xfm --out 200avgsub --subjects* The error: Allocing output mri_concat(40491) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13726th slice Cannot allocate memory WARNING: could not create average segmentation for aseg ... ... but continuing make_average_volume done The average sub folder does not contain aseg.mgz and p.aseg.mgz files. *The version of Freesurfer I am using:* v 1.313.2.6 2010/08/04 15:50:56 nicks *My memory:* 8 GB 1333 MHz DDR3 *Hard-drive:* 276.49 GB free MAC OS X v 10.6.8 I have scoured the archives for the answer to my question to no avail. All of the answers before seemed to revolve around versions of Freesurfer which I expect were updated. Nick Schmanksy wrote sorry, i meant to say include the --no-aseg flag with make_average_volume (make_average_subject is just a wrapper script that calls make_average_volume and make_average_surface). But wouldn't this prevent segmentation? Is there a way to then add segmentation after? Sorry if these are novice questions (as I am a novice). Thank you, Adam ___ 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.
