[FieldTrip] parallelizing ft_statistics_montecarlo to enhance computation speed for time-frequency data

["Jörn M. Horschig"]

Hi Fred,

Matlab is giving mex-files precedence over .m file as long as the 
mex-file is on the path. The easiest ways to check whether Matlab uses 
the mex-file is to type
 >> which combineClusters
that should point to the mex file. Another way to check is to put a 
breakpoint in the beginning of the .m-file, and then call 
combineClusters or run your code. If the mex-file is executed, Matlab 
will not enter the .m-file and thus not arrive and not stop at the 
breakpoint.

However, the files are also in FieldTrip/private, and this is the place 
where other functions that FieldTrip uses are stored. So, actually there 
is no need for you to copy the files over to a separate folder. 
FieldTrip/Matlab should execute the mex-files all by itself already.

Best,
Jörn

On 7/16/2014 3:07 PM, Frédéric Roux wrote:
> Hi Eelke,
>
> thanks for your response - that sounds promising.
>
> I am running fieldtrip-20140527 on a 64 bit Linux server, so I'd
> be keen to give your suggestion a try.
>
> This is actually the first time I am calling mex-files using Matlab,
> but I assume that the way to go is to comment out the part of the code
> in ft_findcluster that combines the cluster and to call the mex-file instead?
>
> If yes, here is what I did: I copied the combineClusters.mexa64 file into
> a spearate folder and added that folder to my Matlab path.
>
> % combine clusters that are connected in neighbouring channel(s)
> % (combinations). Convert inputs to uint32 as that is required by the mex
> % file (and the values will be positive integers anyway).
> addpath('/path2home/mex/');
> cluster = combineClusters(uint32(labelmat), logical(spatdimneighbstructmat), uint32(total));
>
> I am not sure however how to call the mex function. Is this done automatically or do
> I need to add some further steps? May I ask you which approach you are using?
>
> Best,
> Fred
>
>
>
> Frédéric Roux
>
> ----- Original Message -----
> From: "Eelke Spaak" <eelke.spaak at donders.ru.nl>
> To: "FieldTrip discussion list" <fieldtrip at science.ru.nl>
> Sent: Wednesday, July 16, 2014 9:39:03 AM
> Subject: Re: [FieldTrip] parallelizing ft_statistics_montecarlo to enhance computation speed for time-frequency data
>
> Hi Fred,
>
> Some time ago, I replaced parts of the clustering routine with a
> mex-file. For me this greatly sped up the cluster stats. I guess you
> are using a fairly recent (<1yr old) FT version? The platform you're
> using might also be relevant, I just noticed that the mex-file
> (private/combineClusters.mex*) is distributed in compiled form only
> for Linux 64 and Windows 32/64 bit. If you're e.g. on a Macintosh, you
> could compile it yourself from the src/combineClusters.cpp source
> file.
>
> I know of no attempts to parallelise the clustering code.
>
> Best,
> Eelke
>
> On 15 July 2014 17:40, Frédéric Roux <f.roux at bcbl.eu> wrote:
>> Dear all,
>>
>> I would like to ask if anyone has ever tried to speed up the ft_statistics_montecarlo function
>> by using Matlab's parallel computing toolbox ?
>>
>> I would like to run clusterstatistics on time-frequency data, but as a result of the large number
>> of time and frequency bins, the function runs very slowly. So I was thinking to try and modify
>> the code by running the loops over the frequency bins in parallel and see if that could save
>> some time.
>>
>> Before starting to adapt the code on my own, however, I wanted to ask if anyone had ever tried that
>> and also if there could be any possible reasons which would make that this is not a feasible project.
>>
>> Any thoughts or suggestions would be highly appreciated.
>>
>> Best,
>> Fred
>>
>>
>> ---------------------------------------------------------------------------
>>
>>
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-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
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