[FieldTrip] Unsupported data format
Nakyung Lee
rleese12 at berkeley.edu
Sat Jul 16 03:54:29 CEST 2016
Hooray, it works!
Thanks for being patient with me :)
>> 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: discarding non-unique channel names
> In ft_channelselection (line 102)
In ft_selectdata>getselection_chan (line 649)
In ft_selectdata (line 279)
In ft_preprocessing (line 317)
the call to "ft_selectdata" took 2 seconds
preprocessing
preprocessing trial 1 from 1
the call to "ft_preprocessing" took 4 seconds
And thanks again.
Best,
Rachel
On Fri, Jul 15, 2016 at 10:47 AM, Arjen Stolk <a.stolk8 at gmail.com> wrote:
> 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
>>>>>> > _______________________________________________
>>>>>> > fieldtrip mailing list
>>>>>> > fieldtrip at donders.ru.nl
>>>>>> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>>
>>>>>> _______________________________________________
>>>>>> fieldtrip mailing list
>>>>>> fieldtrip at donders.ru.nl
>>>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> fieldtrip mailing list
>>>>> fieldtrip at donders.ru.nl
>>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> fieldtrip mailing list
>>>>> fieldtrip at donders.ru.nl
>>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160715/4c348dd9/attachment-0002.html>
More information about the fieldtrip
mailing list