[FieldTrip] problems with speed of processing

[Bill Budd]

Hi Eliana

 

I see something similar when using SPM8 to process data. I’ve heard that
this might be because SPM8 uses fieldtrip functions to import my continuous
EEG files (Biosemi/bdf) and these functions may not release memory in matlab
after closing. When looping my preprocessing  functions over multiple
subjects I have the exactly same problem in SPM that you see in fieldtrip.
This may not be causing your problem (or mine) but wondered if the
processing your refer to also involves importing raw MEG data?

 

The PCs I’m using have plenty of RAM/disk space (Win7/matlab 2011b).

 

Be great to find a solution to this as it slows done processing multi
subject data significantly!

 

Cheers

 

-Bill

 

 

From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eliana Garcia
Sent: Wednesday, 11 July 2012 2:40 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] problems with speed of processing

 

Dear Stephen,

 

Thanks for the suggestion. I have already one function that is doing all the
preprocessing and saving as well. But this seams not to solve the issue.

 

Thanks,

Eliana

 

On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh
<stephen.whitmarsh at gmail.com> wrote:

Dear Eliana,

 

You could try creating a function that does all this preprocessing and then
writes the output to file.

If you then call this function in a (subject) loop you are sure that Matlab
will free up the memory it used for that function. 

 

Perhaps it helps,

 

Stephen

 

On 10 July 2012 16:57, Eliana Garcia <elilife at gmail.com> wrote:

Hello Dear Fieldtrip Community,

 

I am having now problems with processing my data. I am analyzing a quite big
data set with 400 trials that are composed by 10 sec (re-sampled at 150Hz).
I am doing first a demean, then planar gradient transformation,
time-frequency analysis using multitapers and then combine the planar
gradient again. For the first subject always runs normally, but for the
second one matlab gets really slow. I am taking care in deleting the
variables that I create with big amount of data after I don't need them any
more, so I am using just one big file that is being safe at the end (average
time-frequency across trials) for each of the subjects. Every time matlab
starts to analyze a new subject I am using clear all (with exceptions like
directory and name of subject) but stills with every new subject it gets
slower and slower.

 

Do you have any advises to make the analysis faster? Sometimes is too slow
and the computer normally crashes after 3 subjects.

 

Thank you very much for the attention.

 

Best,


 

-- 

Eliana García Cossio
Applied Neurotechnology Lab.

Graduate School of Neural and Behavioural Science - Max Planck Research
School
Institute of Medical Psychology and Behavioural Neurobiology
Universität Tübingen

(+0049) 01 577-8587604 
Otfried-Müller-Str. 47, 72076 
Tübingen- Germany

 

 

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fieldtrip mailing list
fieldtrip at donders.ru.nl
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-- 

Eliana García Cossio
Applied Neurotechnology Lab.

Graduate School of Neural and Behavioural Science - Max Planck Research
School
Institute of Medical Psychology and Behavioural Neurobiology
Universität Tübingen

(+0049) 01 577-8587604 
Otfried-Müller-Str. 47, 72076 
Tübingen- Germany

 

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