[FieldTrip] FieldTrip data format

Tamang, Sarita sarita.tamang at mssm.edu
Tue Nov 18 15:27:30 CET 2014

Hi All,

I had the same problem as I couldn't convert my LFP data into the field-trip format. I kept getting problems with defining trials. Any input on this would be very helpful.

Thank you,
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Eelke Spaak [eelke.spaak at donders.ru.nl]
Sent: Tuesday, November 18, 2014 7:59 AM
To: Xiong Xiao
Cc: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] FieldTrip data format

Dear Xiong Xiao,

First, in general, I would recommend you send questions like this to
the general FieldTrip mailing list (cc), instead of to any of the
developers personally. Responses on the general list will usually be
faster, and will benefit other FieldTrip users as well. See here:
https://urldefense.proofpoint.com/v2/url?u=http-3A__fieldtrip.fcdonders.nl_discussion-5Flist&d=AAICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=ZGIuqqMPZJ5Zc6lq0reutuU3Ur_DP6HgbiuxMhDx5mw&m=civVQfJg1oAZA4wKjKjNn0Lgoh2q2NTGZYMOnzLs3RM&s=xff7mp7yN1139dfVCzoRkmhWTwB1tTM97tyVCAxNb8U&e=  for instructions how to

Then, I have never worked with the spike data formats, so I cannot
tell you how to import them into FieldTrip. You could have a look at
the various ft_datatype_xxx functions, which outline the structure of
the data format.


On 10 November 2014 15:06, Xiong Xiao <xxiong at ion.ac.cn> wrote:
>   Hi Eelke,
> Sorry to trouble you, but I really want to use FieldTrip for my data
> analysis. I am a graduate student from the Institute of Neuroscience,
> Shanghai. I am a new FieldTrp user with good programming skills. But I
> totally do not know how to convert my raw data (spikes, LFP and events) into
> appropriate format for using FieldTrip. So I converted my data (spikes, LFP
> and events) into .nex format. However, error occured when I read the events
> from .nex files; but it was OK to read spikes.
> BTW, the data was converted to .nex files by using the toolbox provided by
> NeuroExplorer.
> spike = ft_read_spike('xx1_SpikeEvents.nex');
> cfg              = [];
> cfg.spikechannel = {'N1xx1', 'N1xx3'}; % select only the two single units
> spike = ft_spike_select(cfg, spike);
> event = ft_read_event('xx1_SpikeEvents.nex');  % there is error here
> Error message:
> Attempted to access adindx(1); index out of bounds because numel(adindx)=0.
> Error in read_nex_event (line 38)
> smpfrq = hdr.varheader(adindx(1)).wfrequency;
> Error in ft_read_event (line 1528)
>     event = read_nex_event(filename);
> Still I think this is not so convenient to convert my data into .nex files
> and then to process it. Is there some other ways to convert the data into
> appropriate formats?
> The structure of my data is like this:
> (1) Spikes:  cell structure,  { n*1 vector (timestamps) }
> (2) Waveform: cell structure, { n*4*32 matrix (waveforms for tetrodes)}
> (2) Events:   m*2 matrix (the first column is the onset time of events, and
> the second column is the duration of each event)
> (3) LFP: lfp (1*n vector, voltage of the LFP signal), lfp_time (1*n vector,
> time of the LFP signal)
> Thank you for your time.
> Best regards,
> Xiong Xiao
> ________________________________
> *************************************************
> PhD student
> Lab of Neural Circuits and Animal Behavior
> Institute of Neuroscience, Chinese Academy of Sciences
> Room A0738, The New Life Science Building
> 320, Yue Yang Road
> Shanghai 200031, China
> Email: xxiong at ion.ac.cn
> Phone: 86-21-54921769
> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ion.ac.cn_laboratories_int.asp-3Fid-3D46&d=AAICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=ZGIuqqMPZJ5Zc6lq0reutuU3Ur_DP6HgbiuxMhDx5mw&m=civVQfJg1oAZA4wKjKjNn0Lgoh2q2NTGZYMOnzLs3RM&s=SPtddSTcRAxVHLC13eNxpQiAypQksJ9BrQpLZq6h3zU&e=
> *************************************************
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