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
