Dear Nick, Thank you very much for your work. I just came back form Barcelona and tested the mris_make_average_surface and the mri_average (with the -- no-aseg flag) and both worked perfectly fine for my > 400 subjects on the Mac Intel with 5GB RAM.
Thanks a lot, have a nice week, Marie On 7 juin 10, at 21:32, Nick Schmansky wrote: > 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
