Everything is 64bit. I was testing on my local workstation. I'll shift it over to a more powerful system (128gb memory) if you think it is purely a memory issue.
Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Fri, Aug 17, 2018 at 4:42 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > Is everything 64bit? Do you have swap space? > > Matt. > > From: Timothy Hendrickson <hendr...@umn.edu> > Date: Friday, August 17, 2018 at 4:39 PM > To: Timothy Coalson <tsc...@mst.edu> > Cc: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" < > HCP-Users@humanconnectome.org> > Subject: Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run > > It is one participant, with 2950 timepoints and 2mm isotropic voxels. The > machine has 32gb of memory. > > -Tim > > Timothy Hendrickson > Neuroimaging Analyst/Staff Scientist > University of Minnesota Informatics Institute > University of Minnesota > Bioinformatics M.S. Candidate > Office: 612-624-0783 > Mobile: 507-259-3434 (texts okay) > > On Fri, Aug 17, 2018 at 4:32 PM, Timothy Coalson <tsc...@mst.edu> wrote: > >> How much memory does the machine you are running this on have? What is >> the number of timepoints and number of voxels of your concatenated input? >> Are you trying to run more than one subject at once on the machine? >> >> I believe the way we are approaching multi-run fix is that we only >> concatenate scans that were taken on the same day. >> >> Tim >> >> >> On Fri, Aug 17, 2018 at 4:24 PM, Timothy Hendrickson <hendr...@umn.edu> >> wrote: >> >>> Hmm, now I am getting a different error... >>> >>> Elapsed time is 1.67516 seconds. >>> Elapsed time is 2.38414 seconds. >>> >>> error: out of memory or dimension too large for Octave's index type >>> >>> Timothy Hendrickson >>> Neuroimaging Analyst/Staff Scientist >>> University of Minnesota Informatics Institute >>> University of Minnesota >>> Bioinformatics M.S. Candidate >>> Office: 612-624-0783 >>> Mobile: 507-259-3434 (texts okay) >>> >>> On Fri, Aug 17, 2018 at 2:04 PM, Glasser, Matthew <glass...@wustl.edu> >>> wrote: >>> >>>> I have attached an updated version of read_avw_img.m that forces matlab >>>> to retain the same precision as the input file rather than converting >>>> everything to doubles. >>>> >>>> Matt. >>>> >>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy >>>> Hendrickson <hendr...@umn.edu> >>>> Date: Friday, August 17, 2018 at 1:58 PM >>>> To: "hcp-users@humanconnectome.org" <HCP-Users@humanconnectome.org> >>>> Subject: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run >>>> >>>> Hello, >>>> >>>> I am attempting to run FIX cleanup on a rather large dataset (several >>>> fMRI scans concatenated together via hcp_fix_multi_run) and am running into >>>> the following error: >>>> >>>> * In fix_3_clean at 45 * >>>> *Elapsed time is 1.153074 seconds.* >>>> *Elapsed time is 1.077840 seconds.* >>>> *Error using fread* >>>> *Out of memory. Type HELP MEMORY for your options.* >>>> >>>> *Error in read_avw_img (line 24)* >>>> >>>> >>>> >>>> *Error in read_avw (line 34)* >>>> >>>> >>>> >>>> *Error in fix_3_clean (line 63)* >>>> >>>> >>>> >>>> *MATLAB:nomem* >>>> >>>> >>>> How much memory does MATLAB require for this, and is there a way to >>>> change this via an argument? >>>> >>>> -Tim >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>>> >>>> ------------------------------ >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. If you >>>> are not the intended recipient, be advised that any unauthorized use, >>>> disclosure, copying or the taking of any action in reliance on the contents >>>> of this information is strictly prohibited. If you have received this email >>>> in error, please immediately notify the sender via telephone or return >>>> mail. >>>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
