[FieldTrip] Fieldtrip ICA crashes Matlab
Elmeri Syrjänen
elmeri.syrjanen at gmail.com
Wed Apr 2 22:17:51 CEST 2014
Dear Whee Ling,
this is an old bug that has been in FieldTrip since October last year. You
can see the bug report here:
http://bugzilla.fcdonders.nl/show_bug.cgi?id=2316
Safest way to avoid it is to use a mac computer or revert to a FieldTrip
version from September last year.
/elmeri
On Wed, Apr 2, 2014 at 8:47 PM, Hwee Ling Lee <hweeling.lee at gmail.com>wrote:
> Dear Jim,
>
> I figured that the error occurs when I tried to plot the ICA components
> using ft_databrowser, with viewmode as "component".
>
> For the PC, I'm running a 64 bit Windows 7, 32 GB of RAM, and 1000 MB of
> graphics memory (NIVDIA Quadro 600). I've also tried the command on another
> PC running 64 bit Windows 7, Matlab R2012b, 64 GB of RAM and 457 MB of
> graphics memory. Both PCs produced the same internal error that crashes
> Matlab. I was not able to copy the message, as it was a pop out window that
> informs me of the fatal error, and I would have to end the program.
>
> The funny thing was that I was able to plot the ICA components a month
> ago, but not able to. This error occurred once to me as well. I've also
> updated my fieldtrip toolbox to the version on 30 March 2014.
>
> For the Macbook Pro, I did not get this error when I plotted the ICA
> components using the same data and the same commands.
>
> I suspect that it may be a problem with my graphics memory, however, the
> error seems strange to me as it occurs on some times, and the error
> "disappears" on some other times.
>
> I'm contemplating of converting one of my PC to a linux workstation. Do
> you think this will resolve my problems?
>
> Thanks for your help. I'm totally lost here.
>
> Best regards,
> Hweeling
>
>
>
>
> On 2 April 2014 17:10, Herring, J.D. (Jim) <j.herring at fcdonders.ru.nl>wrote:
>
>> Hi Hweeling,
>>
>>
>>
>> Could you please copy and paste the exact error message Matlab is
>> producing? Also, which version (e.g. 2013a) of Matlab are you using?
>>
>>
>>
>> Best,
>>
>>
>>
>> Jim
>>
>>
>>
>>
>>
>>
>>
>> *From:* fieldtrip-bounces at science.ru.nl [mailto:
>> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Hwee Ling Lee
>>
>> *Sent:* maandag 31 maart 2014 17:25
>> *To:* Stephen Politzer-Ahles; FieldTrip discussion list
>> *Subject:* Re: [FieldTrip] Fieldtrip ICA crashes Matlab
>>
>>
>>
>> Hi,
>>
>>
>>
>> Thanks for your reply. I'm running Matlab with 64 bit. I've got 32GB of
>> RAM installed. In the previous month, I was able to run ICA and plot its
>> components without any error message from Matlab. Recently, I keep
>> experiencing the error message, and Matlab crashes completely. I have no
>> clue what could have gone wrong.
>>
>>
>>
>> Cheers,
>>
>> Hweeling
>>
>>
>>
>> On 31 March 2014 17:08, Stephen Politzer-Ahles <politzerahless at gmail.com>
>> wrote:
>>
>> Hello Hweeling,
>>
>>
>>
>> What kind of error do you get in MATLAB when you try to do ICA, is it an
>> "Out of memory" error? I'm asking because this is a fairly common issue in
>> MATLAB on Windows systems (I don't know the details of your data, but I've
>> experienced this issue on 32-channel, 1000-Hz epoched EEG data if the
>> epochs are long enough and numerous enough). For me the only solutions
>> (other than shortening the epochs or downsampling the data, which might not
>> be good options depending on your research question) were to use a
>> Unix-based operating system (like Mac OS) or to upgrade my Windows (I had
>> errors like this when using a 32-bit version of Windows with 2 GB of RAM,
>> but not so much after I upgraded to 64-bit and 8 GB of RAM). I'm not sure
>> if this is the issue you're having, though.
>>
>>
>>
>> Best,
>>
>> Steve
>>
>>
>>
>>
>>
>>
>> Stephen Politzer-Ahles
>> New York University, Abu Dhabi
>> Neuroscience of Language Lab
>> http://www.nyu.edu/projects/politzer-ahles/
>>
>>
>>
>> On Mon, Mar 31, 2014 at 7:02 PM, <fieldtrip-request at science.ru.nl> wrote:
>>
>> Send fieldtrip mailing list submissions to
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>>
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>>
>> When replying, please edit your Subject line so it is more specific
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>>
>> Today's Topics:
>>
>> 1. Fieldtrip ICA crashes Matlab (Hwee Ling Lee)
>> 2. Re: plotting interpolated sources with ft_sourceplot
>> (J?rn M. Horschig)
>> 3. Re: help about ' fieldtrip2fiff ' (Gio Piantoni)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 31 Mar 2014 16:48:34 +0200
>> From: Hwee Ling Lee <hweeling.lee at gmail.com>
>> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
>> Subject: [FieldTrip] Fieldtrip ICA crashes Matlab
>> Message-ID:
>> <CABG7z0SPtmOfGWxqRxiveg+cfUewJ8p8P-v9=
>> poVtb-1ApZuDQ at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Dear all,
>>
>> I'm encountering a problem with running ICA in Matlab. After ICA, when I
>> tried to plot the components, Matlab keeps prompting an internal problem
>> and needs to be closed. I wonder why this is the case. Could someone
>> please
>> tell me what went wrong?
>>
>> Here's part of my script for ICA:
>>
>> cfg = []; % if data were cleaned, then use this
>>
>> if sub == 5 %|| sub == 7
>> cfg.channel = {'all', '-AFz', '-FT7'};
>> elseif sub == 7
>> cfg.channel = {'all' '-AFz'};
>> else
>> cfg.channel = {'all'};
>> end
>>
>> % cfg.runica.pca = 121; % using the rank of my data
>> % ic_data = ft_componentanalysis(cfg,cleandata); % if data were
>> cleaned then use this
>> ic_data = ft_componentanalysis(cfg, cleandata);
>>
>> % after ICA, look for components that we want to substract from
>> our
>> data,
>> % only looking at ten channels (components) at a time
>> cfg = [];
>> cfg.dataset = rawdatafile;
>> cfg.viewmode = 'component';
>> cfg.continuous = 'no';
>> cfg.blocksize = 8;
>> cfg.channels = 'all';
>> cfg.layout = 'EEG1020.lay';
>> ft_databrowser(cfg,ic_data);
>>
>>
>> The internal problem appears even when I downsampled my data from 5000 Hz
>> to 1000 Hz.
>>
>> The internal problem appears also when I have short segments of my data
>> (i.e. 2s per trial), and long segments of my data (i.e. 6s per trial).
>>
>> The memory of my PC workstation is:
>> Maximum possible array: 60253 MB (6.318e+10 bytes) *
>> Memory available for all arrays: 60253 MB (6.318e+10 bytes) *
>> Memory used by MATLAB: 560 MB (5.872e+08 bytes)
>> Physical Memory (RAM): 32685 MB (3.427e+10 bytes)
>>
>> Interestingly, this internal problem does not occur when I ran my script
>> on
>> my Macbook Pro.
>>
>> I'm feeling very lost here. Any help is highly appreciated.
>>
>> Cheers,
>> Hweeling
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>>
>>
>>
>> --
>>
>> =================================================
>> Dr. rer. nat. Lee, Hwee Ling
>> Postdoc
>> German Center for Neurodegenerative Diseases (DZNE) Bonn
>>
>> Email 1: hwee-ling.lee<at>dzne.de
>> Email 2: hweeling.lee<at>gmail.com
>>
>>
>>
>> https://sites.google.com/site/hweelinglee/home
>>
>> Correspondence Address:
>> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
>> =================================================
>>
>
>
>
> --
> =================================================
> Dr. rer. nat. Lee, Hwee Ling
> Postdoc
> German Center for Neurodegenerative Diseases (DZNE) Bonn
>
> Email 1: hwee-ling.lee<at>dzne.de
> Email 2: hweeling.lee<at>gmail.com
>
> https://sites.google.com/site/hweelinglee/home
>
> Correspondence Address:
> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
> =================================================
>
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