<div dir="ltr"><div>Hi,<br><br>So I'm having an issue involving, well I think the issue may not be the downsampling per se, but it does involve attempting to recreate a code similar to the above but in fieldtrip.<br><br>
I'm currently attempting two different methods:<br><br></div><div>1. Method One: Define trials as a cfg_(condition), with the preprocessing parameters contained within the cfg. Then preprocess the cfg_condition. Finally, downsample using ft_resampledata<br>
<br></div><div>2. Method Two: Preprocess the data by channel in a for loop, then concatenate using ft_appenddata, followed by epoching, and finally downsampling. In the original version of this method I downsampled in the for loop, as doing it without downsampling in the loop still strains my computers memory, but when I do that the epoching doesn't seem to work for reasons I partially understand, but in any case can't figure out a workaround for that would be reasonably straightforward.<br>
<br></div><div>In any case, when I do either of these methods, I run into an error:<br><br></div><div>1. For the first method<br></div><div><br>reading and preprocessing trial 1 from 100<br>getCTFdata: dataList error: points=21086:21085 trial=1<br>
points/trial=1584000 No. of trials=1<br><br><br></div><div>2. The Second method<br><br></div><div>Attempted to access data.time.%cell(1); index out of bounds because numel(data.time.%cell)=0.<br><br>Error in ft_resampledata (line 149)<br>
firstsmp(itr) = data.time{itr}(1);<br><br></div><div>Again, I'm not entirely convinced the issue is with downsampling per se, but that is my best guess at the moment. Any help would be greatly appreciated.<br><br>
</div><div>Max Cantor<br>Research Assistant<br>Computational Neurolinguistics Lab<br>University of Michigan<br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jan 16, 2014 at 9:58 AM, Vladimir Litvak <span dir="ltr"><<a href="mailto:litvak.vladimir@gmail.com" target="_blank">litvak.vladimir@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Here it is, just in case some else will need it in the future.</div><div><br></div><div>#!/bin/sh</div>
<div>files=`ls -1Ad ${1}`</div><div><br></div><div>for f in $files</div><div>do</div><div> newSingleTrialDs $f ./s_`basename $f`</div>
<div> newDs -f -filter processing.cfg -resample 8 ./s_`basename $f` ./r_`basename $f`</div><div> rm -rf ./s_`basename $f`</div><div>done</div><div><br></div><div><br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra">
<br><br><div class="gmail_quote">
On Thu, Jan 16, 2014 at 2:51 PM, Frédéric Roux <span dir="ltr"><<a href="mailto:f.roux@bcbl.eu" target="_blank">f.roux@bcbl.eu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Vladimir,<br>
<br>
looks like the shell-script got blocked my the mail-server.<br>
would you mind sending it to <a href="mailto:froux@bcbl.eu" target="_blank">froux@bcbl.eu</a> ?<br>
<br>
Thanks,<br>
<div><br>
Fred<br>
<br>
Frédéric Roux<br>
<br>
----- Original Message -----<br>
</div><div>From: "Vladimir Litvak" <<a href="mailto:litvak.vladimir@gmail.com" target="_blank">litvak.vladimir@gmail.com</a>><br>
To: "FieldTrip discussion list" <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>
</div><div>Sent: Thursday, January 16, 2014 2:28:03 PM<br>
Subject: Re: [FieldTrip] downsampling CTF data prior to ft_preprocessing<br>
<br>
<br>
</div>[Text File:warning1.txt]<br>
<div><div><br>
<br>
<br>
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.<br>
<br>
<br>
Vladimir<br>
<br>
<br>
<br>
On Thu, Jan 16, 2014 at 1:10 PM, Frédéric Roux < <a href="mailto:f.roux@bcbl.eu" target="_blank">f.roux@bcbl.eu</a> > wrote:<br>
<br>
<br>
Hi Vladimir,<br>
<br>
yes now I remember - newDs - will give it a try.<br>
<br>
Thanks a lot everyone for the fast and helpful comments!<br>
<br>
Fred<br>
<br>
<br>
----- Original Message -----<br>
From: "Vladimir Litvak" < <a href="mailto:litvak.vladimir@gmail.com" target="_blank">litvak.vladimir@gmail.com</a> ><br>
To: "FieldTrip discussion list" < <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a> ><br>
<br>
<br>
Sent: Thursday, January 16, 2014 1:57:25 PM<br>
Subject: Re: [FieldTrip] downsampling CTF data prior to ft_preprocessing<br>
<br>
<br>
<br>
Dear Fred,<br>
<br>
<br>
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.<br>
<br>
<br>
Best,<br>
<br>
<br>
Vladimir<br>
<br>
<br>
<br>
On Thu, Jan 16, 2014 at 12:30 PM, Frédéric Roux < <a href="mailto:f.roux@bcbl.eu" target="_blank">f.roux@bcbl.eu</a> > wrote:<br>
<br>
<br>
Hi Jim, Hi Eelke,<br>
<br>
thanks for the fast response.<br>
<br>
My issue is that I would like to use ft_definetrial<br>
to get to my trigger events, hence the reason why<br>
I want to downsample the raw-data before accessing it<br>
with ft.<br>
<br>
But technically, I guess I should be able to write up<br>
my own trigger detection code. It's just more convenient<br>
without having to do that extra step.<br>
<br>
I thought I'd ask before doing that.<br>
<br>
In any case if anyone comes up with an idea how to do the<br>
downsampling on the raw-data, please let me know.<br>
<br>
Best,<br>
Fred<br>
<br>
<br>
<br>
Frédéric Roux<br>
<br>
<br>
----- Original Message -----<br>
From: "J.D. Herring (Jim)" < <a href="mailto:j.herring@fcdonders.ru.nl" target="_blank">j.herring@fcdonders.ru.nl</a> ><br>
To: "FieldTrip discussion list" < <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a> ><br>
Sent: Thursday, January 16, 2014 1:22:07 PM<br>
Subject: Re: [FieldTrip] downsampling CTF data prior to ft_preprocessing<br>
<br>
Hi Fred,<br>
<br>
<br>
If memory is an issue you could try reading-in the data per channel,<br>
resample, and appending afterwards.<br>
<br>
Best,<br>
<br>
Jim<br>
<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a><br>
[mailto: <a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a> ] On Behalf Of Frédéric Roux<br>
Sent: donderdag 16 januari 2014 13:00<br>
To: FieldTrip discussion list<br>
<br>
<br>
Subject: [FieldTrip] downsampling CTF data prior to ft_preprocessing<br>
<br>
Dear all,<br>
<br>
does anyone know of a good method to downsample MEG-data acquired with a<br>
CTF system before reading it into Matlab/fieldtrip.<br>
<br>
I remember that there is a command-line tool provided by CTF which can do<br>
preprocessing, but I don't remember exactly if it does the job.<br>
<br>
Or does anyone know of a good alternative solution?<br>
<br>
Best,<br>
Fred<br>
<br>
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