Marie, The memory leak in mri_average has also been fixed. The new version is in the same ftp location as mris_make_average_surface.
N. On Mon, 2010-06-07 at 14:43 -0400, Nick Schmansky wrote: > Marie, > > I fixed the memory leak that was causing your out-of-memory error when > running mris_make_average_surface. A new mris_make_average_surface for > Mac Intel Leopard is posted here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/ > > I'm still looking into the mri_average failure. I dont know what to say > about the license error, as the code that handles the license hasnt > changed since v2.0. > > As an aside, I'm skeptical of the utility of a volume or surface > composed of 400+ subjects. The volume will be too blurry to be of use, > and the surface will have lost any group-specific patterns that might > have existed. If retaining the unique morphometric properties of your > subject set is important, you might want to consider using just 20 or so > randomly chosen subjects. Perhaps Bruce or others can comment. > > Nick > > > On Wed, 2010-06-02 at 18:53 +0200, Marie Schaer wrote: > > Hi Nick, > > > > Thank you for your response. I added the flag --debug, please find in > > attachment the log. I am working on a Mac Intel Quad-Core Intel Xeon, > > Processor 3 GHz, RAM 5GB. I also tried with another similar machine > > which 9GB, but it exited with the same error exactly at the same > > point. Even using the -no-aseg option it stops exactly at the same > > point. I also provide you a screenshot with the top command running, a > > few minutes before the error, and just after the error. > > > > As for the license error, I just had this problem using the Freesurfer > > version 4.5, and you are right, it may be a connection problem because > > our data are on a server (mounted with afp). It is however strange > > that it exits always at exactly the same point... Anyway, no license > > problem with version 4.4 or 4.3. > > > > Many thanks for your help, > > > > Marie > > > > On 1 juin 10, at 16:54, Nick Schmansky wrote: > > > > > 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
