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Hi Raphael,
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<div class="">If you are unsure about where the slowdown takes place you can evaluate this using the matlab profiler. If you type 'profview on’ a graphical interface to the profiler opens, and you can execute commands, which will then be stopwatched.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 28 Jun 2019, at 14:01, Raphaël Thézé <<a href="mailto:raphael.theze@gmail.com" class="">raphael.theze@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">Dear Jan,
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<div class="">I have tried increasing the java heap memory but the processing still takes ~1 min per individual trial. </div>
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<div class="">Regarding the code, I have tried to break down the different steps, and my impression was that the preproc function was slowing down the whole process, but this is only the case in the fieldtrip version with mff v3. I can try to go over the code
again but the deeper I go into the FT functions, the more confusing it gets!</div>
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<div class="">Thanks for the help, </div>
<div class="">Best</div>
<div class="">Raphaël</div>
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<div dir="ltr" class="gmail_attr">Le jeu. 13 juin 2019 à 18:27, Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>> a écrit :<br class="">
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<div style="overflow-wrap: break-word;" class="">Dear Raphael,
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<div class="">I happened to bump into Trey Avery, from Philips/egi the other day, and he mentioned that you might want to consider to increase the java heap memory to a larger value. How this can be done is shown here: <a href="https://www.mathworks.com/help/matlab/matlab_external/java-heap-memory-preferences.html" target="_blank" class="">https://www.mathworks.com/help/matlab/matlab_external/java-heap-memory-preferences.html</a></div>
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<div class="">That is, in your message you are a bit ambiguous as to where exactly in the code the slowdown takes place. If it is indeed preproc, as you mention, then it’s probably not an input/output problem.</div>
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<div class="">Anyway, it wouldn’t hurt to try I think. Could you let us know whether this works for you? In that case we can add this to our documentation section of ‘getting started with egi data’ on our
<a href="http://fieldtriptoolbox.org/" target="_blank" class="">fieldtriptoolbox.org</a> website. Also, the current version of that part of the documentation could be improved a bit I think to reflect better the recent improvements to the code (i.e. the use
of the v3 reader…). Feel free to suggest changes yourself.</div>
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<div class="">Best wishes,</div>
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<div class="">Jan-Mathijs<br class="">
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<div class="">On 24 May 2019, at 15:58, Raphaël Thézé <<a href="mailto:raphael.theze@gmail.com" target="_blank" class="">raphael.theze@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">Dear all,
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<div class="">I have a question regarding the import of mff file format.</div>
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<div class="">I used to import my EGI data with fieldtrip version 20180201 which worked fine (with egi_mff_v1) but when I switched to fieldtrip version 20190325, it uses egi_mff_v3 as default. The latter also works well except that when it used to take 1 sec
per trial to be imported with V1, now it takes about 1 minute per trial with V3. The amount of time needed to import one subject in my case would be theoretically 3 hours, which is ridiculously long. I understand that the switch of version takes place in ft_read_data,
which is called by ft_preprocessing, but apparently it is preproc, also called by ft_preprocessing, that takes forever to compute, but I can't explain why. I tried to manually request to use the version egi_mff_V1 but then there is an error regarding xml file,
that I have not tried to explore so far. </div>
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<div class="">For now I will just go back to the 20180201 version of fieldtrip so I can quickly import data into matlab, but I would like to understand what is going wrong here, or if it is to be expected. </div>
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<div class="">In advance, thank you all. </div>
<div class="">Best, <br class="">
Raphaël</div>
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