[FieldTrip] Unsupported data format

Fri Jul 15 19:01:07 CEST 2016

Hi Rachel,

Given that you already have the data imported into matlab and organized
into trials, try creating a structure 'data' with the following fields
(i.e. data.label, data.time, data.trial) and the following dimensions:

label: {151x1 cell}      the channel labels (e.g. 'MRC13')
time: {1x266 cell}      the timeaxis [1*Ntime double] per trial
trial: {1x266 cell}      the numeric data [151*Ntime double] per trial

Then, for a proof of principle, try:

cfg = [];
cfg.demean = 'yes';
data2 = ft_preprocessing(cfg, data);

Let us know if this worked for you.
Arjen

2016-07-15 9:51 GMT-07:00 Nakyung Lee <rleese12 at berkeley.edu>:

> Hi Jan-Mathijs,
>
> Thanks for your advice.
> Yes, I used 'ft_=definetrial' to segment the data.
> My data is in the fieldtrip style data format not because it's been
> segmented and preprocessed through fieldtrip but because our original
> dataformat is unsupported by fieldtrip (.Tbk, .Tdx, .tev, .tsq to be exact).
> So my coworker transformed those data into a .mat file and I transformed
> into a fieldtrip style raw data but it still needs some segmenting and some
> other preprocessing done on it (for example high-gamma filtering).
> But if 'ft_preprocessing' is only useable when reading proprietary data
> from disk, there's just no way we can preprocess the above data using
> fieldtrip?
>
> Thank you,
> Rachel
>
> On Fri, Jul 15, 2016 at 1:10 AM, Schoffelen, J.M. (Jan Mathijs) <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Rachel,
>>
>> Once your data is represented in a fieldtrip-style structure, there’s no
>> need anymore to call ft_definetrial with a specified named dataset in the
>> cfg.
>>
>> If you want to segment your data, you may still want to call
>> ft_definetrial to generate a so-called ‘trl’ matrix, and subsequently use
>> ft_redefinetrial to re-segment, i.e.:
>>
>> load(’signal_raw.mat’); % I assume that this files contains the
>> fieldtrip-style data structure
>>
>> cfg = [];
>> cfg.trl = trl;
>> data_epoched = ft_redefinetrial(cfg, data);
>>
>> So, note that ft_preprocessing shouldn’t be called, this is onlyl useable
>> when reading proprietary data from disk.
>>
>> It seems that you don’t need the cfg.dataset argument to begin with, and
>> if you manage to titrate your ft_trialfun_test such that it converts the
>> timestamps you provide it with into the correct trl-matrix, I don’t see a
>> reason why it shouldn’t work.
>>
>> Best,
>> Jan-Mathijs
>>
>>
>> On 15 Jul 2016, at 08:49, Nakyung Lee <rleese12 at berkeley.edu> wrote:
>>
>> Hi Arjen,
>>
>> Thank you for your reply.
>> Your email got forwarded successfully.
>>
>> So currently I tried using 'ft_definetrial' and 'ft_preprocessing'.
>> 'ft_definetrial' returns an error when used with 'ft_trialfun' set to
>> default.
>> Below is the code I used (and 'signal_raw.mat' is a fieldtrip raw data
>> and it has all three fields you mentioned).
>>
>> cfg.dataset = 'signal_raw.mat';
>> cfg.trialdef.event = subj_globals.buttonpress_times;
>> cfg = ft_definetrial(cfg);
>>
>> So I simply call ft_definetrial with minimal configuration and here's the
>> error I got:
>>
>> Error using ft_read_header (line 2194)
>> unsupported header format "matlab"
>>
>> Error in ft_trialfun_general (line 78)
>> hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat);
>>
>> Error in ft_definetrial (line 177)
>>     [trl, event] = feval(cfg.trialfun, cfg);
>>
>> Error in trialdef_alsotest (line 12)
>> cfg = ft_definetrial(cfg);
>>
>> I circumvented this issue by using my own trialfun ('ft_trialfun_test' in
>> the code).
>> We already have all the necessary timestamps so I could build a very
>> simple one.
>> Here's a new code (I ran the code with minimal cfg for 'ft_preprocessing'
>> to isolate the problem):
>>
>> cfg.dataset = 'signal_raw.mat';
>> cfg.trialfun = 'ft_trialfun_test';
>> cfg.trialdef.event = subj_globals.buttonpress_times;
>>
>> cfg = ft_definetrial(cfg);
>>
>> cfg.continuous = 'yes';
>> buttonpress_hg = ft_preprocessing(cfg);
>>
>> And here's the error I got:
>>
>> Error using ft_read_header (line 2194)
>> unsupported header format "matlab"
>>
>> Error in ft_preprocessing (line 397)
>>   hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat,
>> 'coordsys', cfg.coordsys, 'coilaccuracy',
>>   cfg.coilaccuracy);
>>
>> Error in test_trialdef (line 18)
>> buttonpress_hg = ft_preprocessing(cfg);
>>
>> So both error come from 'ft_read_header'.
>> I've been looking at the code but it seemed quite hard to debug as
>> 'ft_read_header' uses a lower level function that directly reads from the
>> file (hence it seemed like a simple fix like passing in a fake header
>> wouldn't work).
>> Am I doing something wrong here?
>>
>> Again, thank you for your reply and let me know if you need more
>> information.
>>
>> Best,
>> Rachel
>>
>> On Thu, Jul 14, 2016 at 12:10 AM, Arjen Stolk <a.stolk8 at gmail.com> wrote:
>>
>>> Hi Rachel,
>>>
>>> What is the error you're receiving, and how are you calling
>>> ft_preprocessing?
>>>
>>> If the data is in raw format (incl a trial, time and label field), it
>>> should theoretically be possible to use ft_preprocessing on it, eg;
>>> cfg = []
>>> cfg ..
>>> data = ft_preprocessing(cfg, raw)
>>>
>>> where raw is your data as described above.
>>>
>>> Best,
>>> Arjen
>>>
>>> > On Jul 13, 2016, at 11:50 PM, Nakyung Lee <rleese12 at berkeley.edu>
>>> wrote:
>>> >
>>> > Dear FieldTrip community,
>>> >
>>> > My name is Rachel Lee and I'm a research assistant in Prof. Ming Hsu's
>>> lab in UC Berkeley.
>>> >
>>> > We currently have a .Tbk file, a .Tdx file, .tev file, .tsq file to
>>> preprocess and analyze but it seems like those data formats are not yet
>>> supported by FieldTrip.
>>> > So, instead of using those raw data files, we've been trying to find a
>>> workaround by transforming them into a .mat file (and casting the .mat file
>>> into a raw datatype in FieldTrip by manually assigning fields to it).
>>> > This hasn't been so successful; we've been unable to call
>>> ft_preprocessing because of the lack of a proper header format (which is
>>> needed in ft_read_header, one of the lower level functions that
>>> ft_preprocessing calls).
>>> > I've been looking at the codes but been unable to come up with a
>>> solution.
>>> >
>>> > Does anyone have a similar experience?
>>> > Is there any way to circumvent this issue?
>>> > Any type of help would be appreciated.
>>> >
>>> > Thank you,
>>> > Rachel Lee
>>> > _______________________________________________
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>>> > fieldtrip at donders.ru.nl
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>>
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