[FieldTrip] Unsupported data format

Fri Jul 15 19:47:39 CEST 2016

Almost there, Rachel. :) Now ensure your data.label field contains strings
and not numbers, i.e.

data.label = {'1';'2'} and not {1;2}

2016-07-15 10:33 GMT-07:00 Nakyung Lee <rleese12 at berkeley.edu>:

> Hi Arjen,
>
> Yes, that is exactly the structure of 'signal_raw' I'm using.
> I tried your code (without running 'ft_definetrial' beforehand) and here's
> the log:
>
> >> cfg = [];
> >> cfg.demean = 'yes';
> >> data = signal_raw
>
> data =
>
>       label: {176x1 cell}
>        time: {[1x721186 double]}
>       trial: {[176x721186 double]}
>     fsample: 1000
>
> >> data2 = ft_preprocessing(cfg, data);
> Warning: the data does not contain a trial definition
> > In ft_warning (line 184)
>   In fixsampleinfo (line 66)
>   In ft_datatype_raw (line 175)
>   In ft_checkdata (line 219)
>   In ft_preprocessing (line 274)
> Warning: reconstructing sampleinfo by assuming that the trials are
> consecutive segments of a continuous recording
> > In ft_warning (line 184)
>   In fixsampleinfo (line 79)
>   In ft_datatype_raw (line 175)
>   In ft_checkdata (line 219)
>   In ft_preprocessing (line 274)
> Error using cell/ismember (line 34)
> Input A of class cell and input B of class cell must be cell arrays of
> strings, unless one is a string.
>
> Error in ft_senstype (line 303)
>     if     (mean(ismember(ft_senslabel('ant128'),         sens.label)) >
> 0.8)
>
> Error in ft_channelselection (line 83)
>   senstype = ft_senstype(datachannel);
>
> Error in ft_selectdata>getselection_chan (line 649)
>   selchannel = ft_channelselection(cfg.channel, varargin{k}.label);
>
> Error in ft_selectdata (line 279)
> if haschan,    [selchan,    cfg] = getselection_chan   (cfg, varargin{:},
> cfg.select); end
>
> Error in ft_preprocessing (line 317)
>   data   = ft_selectdata(tmpcfg, data);
>
> This data is not segmented yet so there's only one trial (and hence time: {[1x721186
> double]} and trial: {[176x721186 double]}) with 'Ntime' equal to '721186'.
> There were warning signs but seems like those are ignore-able ones.
> Again, let me know if you need more information and thank you.
>
> Best,
> Rachel
>
> On Fri, Jul 15, 2016 at 10:01 AM, Arjen Stolk <a.stolk8 at gmail.com> wrote:
>
>> 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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>>>>
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