Hi Doug Thanks for the new version of make_average_surface. I tried it but the old error came back again:
Allocing output mri_concat(28362) 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 13930th slice Cannot allocate memory [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% Sorry Regards Juergen On 11.2.2008 18:52 Uhr, "Doug Greve" <[EMAIL PROTECTED]> wrote: > The problem is that it is calling mris_preproc with --srcsurfreg, and you do > not have the version of mris_preproc that accepts this flag. You can edit it > to make it --surfreg. Or, you can get a new copy of make_average_surface from: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_sur > face > > doug > > Juergen Haenggi wrote: >> Re: [Freesurfer] Problem make_average_subject Hi Doug >> >> Thanks a lot for the new version of the make_average_subject scripts. I tried >> it but the following error occurred: >> >> Reading surface >> /Applications/freesurfer/subjects/average/surf/rh.white >> Loading annotations from >> /Applications/freesurfer/subjects/average/label/rh.aparc.a2005s.annot >> max index = 81 >> 3 387 >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_ci >> ngulate-Isthmus.label >> LabelWrite: saving to >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_ci >> ngulate-Isthmus.label >> 4 2350 >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_ci >> ngulate-Main_part.label >> LabelWrite: saving to >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_ci >> ngulate-Main_part.label >> 5 1412 >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_cu >> neus.label >> LabelWrite: saving to >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_cu >> neus.label >> 6 1479 >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_fr >> ontal_inf-Opercular_part.label >> LabelWrite: saving to >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.G_fr >> ontal_inf-Opercular_part.label >> . >> . >> . >> . >> . >> LabelWrite: saving to >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_su >> borbital.label >> 77 1999 >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_su >> bparietal.label >> LabelWrite: saving to >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_su >> bparietal.label >> 79 1276 >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te >> mporal_inferior.label >> LabelWrite: saving to >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te >> mporal_inferior.label >> 80 7673 >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te >> mporal_superior.label >> LabelWrite: saving to >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te >> mporal_superior.label >> 81 365 >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te >> mporal_transverse.label >> LabelWrite: saving to >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236/rh.S_te >> mporal_transverse.label >> mri_mergelabels -o >> /Applications/freesurfer/subjects/average/label/rh.cortex.label -d >> /Applications/freesurfer/subjects/average/make_cortex_label.tmp.69236 >> Done >> /Applications/freesurfer/subjects/average/surf >> mris_preproc --out rh.orig.avg.area.mgh --f /tmp/subjlist.69236 --target >> average --hemi rh --area orig --mean --srcsurfreg sphere.reg >> ERROR: flag --srcsurfreg not recognized >> [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% >> >> It seems that there is a index maximum of 81 and therefore the flag >> --srcsurfreg is not recognized. >> >> Thanks >> Regards >> Juergen >> >> >> On 6.2.2008 23:05 Uhr, "Doug Greve" <[EMAIL PROTECTED]> >> <mailto:[EMAIL PROTECTED]> wrote: >> >> >>> >>> I think the failure happens when it tries to create the group aseg.mgz. I >>> changed the code on 1/3/08 so that it would just print a warning and >>> continue, but I don't think this version is being distributed yet. >>> >>> I've put new versions of >>> make_average_subject make_average_surface make_average_volume >>> >>> here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve >>> >>> Copy them into $FREESURFER_HOME/bin (make backups:), and give it a try. >>> >>> doug >>> >>> >>> >>> James N. Porter wrote: >>> >>>> So, I believe I have isolated the problem. The failure happens during the >>>> mri_concat phase of make_average_volumes. The seg-subj#.mgh temp files that >>>> are being concatenated are 65 MB each and I can successfully run 59 >>>> subjects, but for 60 subjects and up, mri_concat exits immediately with the >>>> error message as written below. I have 4GB of memory, and 65*59 is less >>>> than 4 GB so that works; add any more subjects and the process is shut >>>> down. It appears that mri_concat checks to see how much memory will be >>>> needed to hold all those .mgh files in active use, then checks the machine >>>> to see how much physical memory is available. I can easily set up a larger >>>> swap file to handle the full 175*65 that is needed (it will be insanely >>>> slow, but that's better than nothing). However, I can't get FreeSurfer to >>>> utilize the swap space I already have available. >>>> >>>> I watched the whole make_average_volumes process play out on my resource >>>> monitor (I imagine that's what watching NASCAR is like--Come on, just crash >>>> already!) and while it came very close to using all 4GB--leaving a paltry >>>> 19 MB free at most points--it didn't touch the swap at any point during the >>>> run. This is not the case with Matlab and other programs, which will >>>> greedily eat up physical memory then seek out the swap. While I appreciate >>>> that the FreeSurfer programs are set up to be judicious consumers of >>>> resources, is there some sort of environmental variable in FreeSurfer or >>>> line of code in mri_concat that I can modify that would allow the programs >>>> to reach out and use the swap space? >>>> >>>> Thanks, >>>> Jim >>>> >>>> --------- >>>> Jim Porter >>>> Graduate Student >>>> Clinical Science & Psychopathology Research >>>> University of Minnesota >>>> >>>> >>>> >>>> >>>> >>>> James N. Porter wrote: >>>> >>>>> Juergen--Have you had successful resolution to this problem? >>>>> >>>>> Nick--I'm attempting to average 175 subjects, but make_average_volume >>>>> returns the same error as Juergen reports. >>>>>> > Allocing output >>>>>> > MRIalloc(256,256,256): could not allocate 262144 bytes for 15547th slice >>>>> >>>>> I'm running freesurfer-Linux-rh9-stable-pub-v4.0.1 on SUSE Linux 9.3 >>>>> 2.6.11.4-21.17-smp x86_64, with a pair of Pentium 3.20 GHz processors, 4 >>>>> GB of physical memory and 8 GB of swap memory. My limits are also quite >>>>> liberal. >>>>>> > cputime unlimited >>>>>> > filesize unlimited >>>>>> > datasize unlimited >>>>>> > stacksize unlimited >>>>>> > coredumpsize 0 kbytes >>>>>> > memoryuse unlimited >>>>>> > vmemoryuse unlimited >>>>>> > descriptors 1024 >>>>>> > memorylocked 32 kbytes >>>>>> > maxproc 28660 >>>>> >>>>> I've tried to also use the alternative script posted by Doug Greve >>>>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html) >>>>> . >>>>> <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html% >>>>> 29.> That also returns the same error. >>>>> >>>>> Any suggestions? >>>>> >>>>> Many thanks, >>>>> >>>>> --------- >>>>> Jim Porter >>>>> Graduate Student >>>>> Clinical Science & Psychopathology Research >>>>> University of Minnesota >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Nick Schmansky wrote: >>>>> >>>>>> >>>>>> Juergen, >>>>>> >>>>>> Edit the 'make_average_subject' script removing (or commenting-out) the >>>>>> line 'limit descriptors unlimited'. You may have to do the same for >>>>>> 'make_average_surface' and 'make_average_volume'. Although in v4.0, >>>>>> these should already be commented-out. >>>>>> >>>>>> Nick >>>>>> >>>>>> On Mon, 2008-01-28 at 16:29 +0100, Juergen Haenggi wrote: >>>>>> >>>>>> >>>>>> >>>>>>> >>>>>>> Dear FS experts >>>>>>> >>>>>>> I tried to run make_average_subject in the past with 92 subjects and got >>>>>>> the >>>>>>> following error: Cannot allocate memory. This is now on the to-do list >>>>>>> of >>>>>>> the FS website. Then I bought some additional RAM and changed from OS X >>>>>>> tiger to leopard. Now I tried it again and get this error: >>>>>>> >>>>>>> [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit >>>>>>> descriptors 4096 >>>>>>> [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit >>>>>>> cputime unlimited >>>>>>> filesize unlimited >>>>>>> datasize 6144 kbytes >>>>>>> stacksize 8192 kbytes >>>>>>> coredumpsize 0 kbytes >>>>>>> memoryuse unlimited >>>>>>> descriptors 4096 >>>>>>> memorylocked unlimited >>>>>>> maxproc 266 >>>>>>> [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% >>>>>>> make_average_subject --subjects SNPs_Vp* >>>>>>> limit: descriptors: Can't remove limit (Invalid argument) >>>>>>> [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% >>>>>>> >>>>>>> I set the descriptor limit to 4096, but the make_average_subject command >>>>>>> will not start anymore. >>>>>>> >>>>>>> Any idea what is wrong here? >>>>>>> >>>>>>> Thanks in advance >>>>>>> Best regards >>>>>>> Juergen >>>>>>> >>>>>>> ----------------------------------------------------------- >>>>>>> Juergen Haenggi >>>>>>> Ph.D. (Dr. des.) >>>>>>> Division of Neuropsychology >>>>>>> Institute of Psychology >>>>>>> University of Zurich >>>>>>> Binzmuehlestrasse 14, PO Box 25 >>>>>>> 8050 Zurich, Switzerland >>>>>>> 0041 44 635 73 97 (phone office) >>>>>>> 0041 76 445 86 84 (phone mobile) >>>>>>> 0041 44 635 74 09 (fax office) >>>>>>> BIN 4.D.04 (office room number) >>>>>>> [EMAIL PROTECTED] (email) >>>>>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>>>>> http://www.juergenhaenggi.ch (private website) >>>>>>> ----------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>> >>> >> >> >> >> ----------------------------------------------------------- >> Juergen Haenggi >> Ph.D. (Dr. des.) >> Division of Neuropsychology >> Institute of Psychology >> University of Zurich >> Binzmuehlestrasse 14, PO Box 25 >> 8050 Zurich, Switzerland >> 0041 44 635 73 97 (phone office) >> 0041 76 445 86 84 (phone mobile) >> 0041 44 635 74 09 (fax office) >> BIN 4.D.04 (office room number) >> [EMAIL PROTECTED] (email) >> http://www.psychologie.uzh.ch/neuropsy/ (website) >> http://www.juergenhaenggi.ch (private website) >> ----------------------------------------------------------- >> >> ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [EMAIL PROTECTED] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------
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