<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">FieldTrip Experts -<div><br></div><div>I'm building a FieldTrip pipeline for use on M/EEG data collected on a Neuromag 306 system. Because I'm looping over subjects (13 currently), event type (5 unique events), and number of runs (4), there's lots of preprocessing to do. After processing a certain amount of files, MATLAB refuses to open more files. </div><div><br></div><div>I ran 'lsof MATLAB | grep "/autofs/cluster/kuperberg/" (to only include the data files I'm using, not MATLAB's system files) and found that for every innermost loop, my script is opening the .fif file twice and not releasing it. I use a custom function for ft_definetrial and in that I use ft_read_event (that operates on the .fif file). After defining trials, I use ft_preprocessing.</div><div><br></div><div>I would venture to guess that both ft_read_event and ft_read_data (ft_preprocessing:line 492) are either 1) not closing files they've opened (presumably through MNE functions), or 2) they're using shared code that doesn't close files. I use MNE and haven't run into this issue before. That being said, fclose('all') does close all these files but I think it's still worth looking into.</div><div><br></div><div>FWIW I'm using CentOS 5 and MATLAB R2010B (glnxa64).</div><div><br></div><div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Scott Burns</div><div>Kuperberg Lab</div><div>Martinos Center for Biomedical Imaging</div><div><a href="mailto:sburns@nmr.mgh.harvard.edu">sburns@nmr.mgh.harvard.edu</a></div><div><br></div><div><span class="Apple-style-span" style="border-collapse: collapse; "><font class="Apple-style-span" face="Arial" size="1"><span class="Apple-style-span" style="font-size: 9px; ">The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at </span></font><a href="http://www.partners.org/complianceline" target="_blank"><font class="Apple-style-span" face="Arial" size="1"><span class="Apple-style-span" style="font-size: 9px; "><font class="Apple-style-span" color="#000000">http://www.partners.org/<wbr>complianceline</font></span></font></a><font class="Apple-style-span" face="Arial" size="1"><span class="Apple-style-span" style="font-size: 9px; "> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.</span></font></span></div><div><br></div></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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