Is everything 64bit? Do you have swap space? Matt.
From: Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Friday, August 17, 2018 at 4:39 PM To: Timothy Coalson <[email protected]<mailto:[email protected]>> Cc: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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: <[email protected]<mailto:[email protected]>> on behalf of Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Friday, August 17, 2018 at 1:58 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> 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 [email protected]<mailto:[email protected]> 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
