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]> 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]> > 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]> on behalf of Timothy >> Hendrickson <[email protected]> >> Date: Friday, August 17, 2018 at 1:58 PM >> To: "[email protected]" <[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] >> 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
