[FieldTrip] downsampling CTF data prior to ft_preprocessing

[Frédéric Roux]

Thanks Vladimir, this is very helpful.

Best,
Fred

----- Original Message -----
From: "Vladimir Litvak" <litvak.vladimir at gmail.com>
To: "FieldTrip discussion list" <fieldtrip at science.ru.nl>
Sent: Thursday, January 16, 2014 3:58:31 PM
Subject: Re: [FieldTrip] downsampling CTF data prior to ft_preprocessing




Here it is, just in case some else will need it in the future. 


#!/bin/sh 
files=`ls -1Ad ${1}` 


for f in $files 
do 
newSingleTrialDs $f ./s_`basename $f` 
newDs -f -filter processing.cfg -resample 8 ./s_`basename $f` ./r_`basename $f` 
rm -rf ./s_`basename $f` 
done 







On Thu, Jan 16, 2014 at 2:51 PM, Frédéric Roux < f.roux at bcbl.eu > wrote: 


Hi Vladimir, 

looks like the shell-script got blocked my the mail-server. 
would you mind sending it to froux at bcbl.eu ? 

Thanks, 


Fred 

Frédéric Roux 

----- Original Message ----- 

From: "Vladimir Litvak" < litvak.vladimir at gmail.com > 
To: "FieldTrip discussion list" < fieldtrip at science.ru.nl > 

Sent: Thursday, January 16, 2014 2:28:03 PM 
Subject: Re: [FieldTrip] downsampling CTF data prior to ft_preprocessing 


[Text File:warning1.txt] 





Here is my old code. Actually the config file is just for filtering but I think you must low-pass before downsampling as it won't do it automatically. It might do more than you need as I also had to convert pseudo-epoched to continuous data. 


Vladimir 



On Thu, Jan 16, 2014 at 1:10 PM, Frédéric Roux < f.roux at bcbl.eu > wrote: 


Hi Vladimir, 

yes now I remember - newDs - will give it a try. 

Thanks a lot everyone for the fast and helpful comments! 

Fred 


----- Original Message ----- 
From: "Vladimir Litvak" < litvak.vladimir at gmail.com > 
To: "FieldTrip discussion list" < fieldtrip at science.ru.nl > 


Sent: Thursday, January 16, 2014 1:57:25 PM 
Subject: Re: [FieldTrip] downsampling CTF data prior to ft_preprocessing 



Dear Fred, 


The CTF command line tool is called newDs . There is a configuration file that you should set-up to specify that you want it to downsample. I used it a long time ago but I can try to find out more details if you can't figure it out yourself. The documentation for the function should be in CTF PDF files. 


Best, 


Vladimir 



On Thu, Jan 16, 2014 at 12:30 PM, Frédéric Roux < f.roux at bcbl.eu > wrote: 


Hi Jim, Hi Eelke, 

thanks for the fast response. 

My issue is that I would like to use ft_definetrial 
to get to my trigger events, hence the reason why 
I want to downsample the raw-data before accessing it 
with ft. 

But technically, I guess I should be able to write up 
my own trigger detection code. It's just more convenient 
without having to do that extra step. 

I thought I'd ask before doing that. 

In any case if anyone comes up with an idea how to do the 
downsampling on the raw-data, please let me know. 

Best, 
Fred 



Frédéric Roux 


----- Original Message ----- 
From: "J.D. Herring (Jim)" < j.herring at fcdonders.ru.nl > 
To: "FieldTrip discussion list" < fieldtrip at science.ru.nl > 
Sent: Thursday, January 16, 2014 1:22:07 PM 
Subject: Re: [FieldTrip] downsampling CTF data prior to ft_preprocessing 

Hi Fred, 


If memory is an issue you could try reading-in the data per channel, 
resample, and appending afterwards. 

Best, 

Jim 


-----Original Message----- 
From: fieldtrip-bounces at science.ru.nl 
[mailto: fieldtrip-bounces at science.ru.nl ] On Behalf Of Frédéric Roux 
Sent: donderdag 16 januari 2014 13:00 
To: FieldTrip discussion list 


Subject: [FieldTrip] downsampling CTF data prior to ft_preprocessing 

Dear all, 

does anyone know of a good method to downsample MEG-data acquired with a 
CTF system before reading it into Matlab/fieldtrip. 

I remember that there is a command-line tool provided by CTF which can do 
preprocessing, but I don't remember exactly if it does the job. 

Or does anyone know of a good alternative solution? 

Best, 
Fred 

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