[FieldTrip] EGI mff file import

Raphaël Thézé raphael.theze at gmail.com
Fri Jun 28 14:01:32 CEST 2019


Dear Jan,

I have tried increasing the java heap memory but the processing still takes
~1 min per individual trial.

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!

Thanks for the help,
Best
Raphaël

Le jeu. 13 juin 2019 à 18:27, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> a écrit :

> Dear Raphael,
>
> 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:
> https://www.mathworks.com/help/matlab/matlab_external/java-heap-memory-preferences.html
>
> 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.
>
> 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 fieldtriptoolbox.org 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.
>
> Best wishes,
>
> Jan-Mathijs
>
> On 24 May 2019, at 15:58, Raphaël Thézé <raphael.theze at gmail.com> wrote:
>
> Dear all,
>
> I have a question regarding the import of mff file format.
>
> 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.
>
> 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.
>
> In advance, thank you all.
> Best,
> Raphaël
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