Okay I have gotten past the previous issue with read_avg, however, I am experiencing a new error.
See below: Error using call_fsl (line 36) FSL call (/bin/sh -c '. /usr/local/fsl/etc/fslconf/fsl.sh; fslcpgeom filtered_func_data filtered_func_data_clean') failed, Unable to allocate memory for copy: Cannot allocate memory Error in fix_3_clean (line 112) On Fri, Aug 17, 2018 at 4:53 PM, Timothy Coalson <tsc...@mst.edu> wrote: > In other words, if you have matlab installed, set the matlab mode to 1 (in > settings.sh). If not, you will need the compiled matlab to be up to date > with the matlab scripts, and use mode 0. > > The alternative, figuring out how to build octave to handle larger > matrices, sounds like an adventure. > > Tim > > > On Fri, Aug 17, 2018 at 4:50 PM, Timothy Coalson <tsc...@mst.edu> wrote: > >> It looks like default builds of octave have an unfortunate limit to the >> possible number of elements in any matrix: >> >> octave:1> test=zeros(60000); >> error: out of memory or dimension too large for Octave's index type >> >> The limit appears to be 2 billion elements total (signed 32-bit). >> >> Tim >> >> >> 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
