[FieldTrip] access to GDF file
Sina Makhdoomi Kaviri
sinam1 at umbc.edu
Thu May 2 21:09:17 CEST 2024
This is another way I tried to access the exact data:
>> EEGLABFILE = './dataset/S3R1.set';
>> hdr = ft_read_header( EEGLABFILE );
data = ft_read_data( EEGLABFILE, 'header', hdr );
events = ft_read_event( EEGLABFILE, 'header', hdr );
>> cfg = [];
cfg.datafile = data;
cfg.headerfile = hdr;
>> cfg.trialdef.eventtype = '1541'; % get a list of the
available types
cfg.trialfun = 'ft_trialfun_general';
cfg.trialdef.triallength = 1; % duration in seconds
cfg = ft_definetrial(cfg);
Error using isfolder
Input path must be text.
Error in ft_filetype (line 166)
if isfolder(filename)
Error in ft_checkconfig (line 690)
cfg.dataformat = ft_filetype(cfg.datafile);
Error in ft_definetrial (line 131)
cfg = ft_checkconfig(cfg, 'dataset2files', 'yes');
On Thu, May 2, 2024 at 3:04 PM Sina Makhdoomi Kaviri <sinam1 at umbc.edu>
wrote:
> On the other hand, I would like to note that I have access to event types
> by biosig in EEGLAB, but how can I convert the data to the fieldtrip as
> well because as I mentioned there appear some errors after reading it in
> fieldtrip.
>
> On Thu, May 2, 2024 at 2:50 PM Sina Makhdoomi Kaviri <sinam1 at umbc.edu>
> wrote:
>
>> Hi,
>> Thanks for your response and consideration.
>> I am still waiting for an effective reply, meanwhile I tried different
>> codes to access the event code and how I can preprocess this data
>> initially, so I use the following code and you can see the warning.
>> >> dataset = './dataset/S03_ME/motorexecution_subject3_run1.gdf';
>> >> hdr = ft_read_header(dataset);
>> data = ft_read_data(dataset, 'header', hdr );
>> events = ft_read_event(dataset, 'header', hdr );
>> Warning: BIOSIG does not have a consistent event representation, skipping
>> events
>>
>> On Thu, May 2, 2024 at 2:46 PM Schoffelen, J.M. (Jan Mathijs) via
>> fieldtrip <fieldtrip at science.ru.nl> wrote:
>>
>>> Hi,
>>>
>>> As you may have already found in the fieldtrip documentation in
>>> https://fieldtriptoolbox.org
>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffieldtriptoolbox.org%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C041d95ebd14c4d74a35b08dc6ad7c2fd%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638502722122927280%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=e3lKBaeNOr78IAhf0y%2FWHS25AkWaWyd6VXz0CwNucyE%3D&reserved=0>,
>>> events are read in by the function ft_read_event.
>>>
>>> I guess you have already started inspecting the code in ft_read_event
>>> using the MATLAB debugger, and you may have found the relevant lines
>>> 484-504 dealing with the .gdf file format.
>>>
>>> I assume (although you did not explicitly mention this) that
>>> ft_read_event in the case of the dataset that you mentioned returns an
>>> empty event structure, which means that you will have had the warning on
>>> your screen that is in line 500. In other words, based the specific data
>>> organization in the file, FieldTrip does not know how to interpret the
>>> trigger information.
>>>
>>> Continuing the detective work, you will have noticed that in line 492
>>> the function ft_read_header is called, producing a variable hdr, based on
>>> which consecutively a ’statusindex’ is determined, which consecutively
>>> determines whether or not the warning is thrown. Now, if we take a close
>>> look at the section in ft_read_header that deals with .gdf files, you will
>>> see in line 1545 that the read_biosig_header function is used to read in
>>> the metadata from the datafile. The read_biosig_header function uses
>>> biosig’s sopen function to do the heavy lifting.
>>>
>>> Apparently, there has never been somebody who managed to write some
>>> ‘glue code’ that translates the events which are not represented on a
>>> digital STATUS channel into a representation that FieldTrip can work with.
>>>
>>> We look forward to a generic implementation that broadcasts the events
>>> from the biosig header to FieldTrip as an improvement to be able to deal
>>> with a broader selection of .gdf files. Please submit your suggested code
>>> changes as a PR to our toolbox’s repository on github, which is located at
>>> https://github.com/fieldtrip/fieldtrip
>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C041d95ebd14c4d74a35b08dc6ad7c2fd%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638502722122927280%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=VgMRfCSYwh76Csyl1ftaNVdeTVu%2Bfjh9fxSMxWlYaj8%3D&reserved=0>
>>> .
>>>
>>> Best wishes and happy coding,
>>> Jan-Mathijs
>>>
>>>
>>>
>>> On 2 May 2024, at 19:04, Sina Makhdoomi Kaviri via fieldtrip <
>>> fieldtrip at science.ru.nl> wrote:
>>>
>>> I want to add this note that if I uploaded the dataset into the
>>> fieldtrip directly, it does not recognize the dataset related to specific
>>> event type. Please help me how can I access the event code in this dataset
>>> and separate it to process in the beamforming method. Here is my code:
>>> dataset = './dataset/S03_ME/motorexecution_subject3_run1.gdf';
>>> cfg = [];
>>> cfg.dataset = dataset;
>>> cfg.trialdef.eventtype = '1541'; % get a list of the available types
>>> cfg.trialfun = 'ft_trialfun_general';
>>> cfg.trialdef.triallength = 1; % duration in seconds
>>> cfg = ft_definetrial(cfg);
>>> cfg.dftfreq = [50];
>>> cfg.channel = 'EEG';
>>> data_segmented = ft_preprocessing(cfg);
>>>
>>>
>>> On Thu, May 2, 2024 at 11:16 AM Sina Makhdoomi Kaviri <sinam1 at umbc.edu>
>>> wrote:
>>>
>>>> To whom it may concern,
>>>>
>>>> I want to implement, "A novel explainable machine learning approach for
>>>> EEG-based brain computer interface systems" published in Springer Nature,
>>>> in fieldtrip. Regarding that they used (
>>>> http://bnci-horizon-2020.eu/database/data-sets
>>>> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbnci-horizon-2020.eu%2Fdatabase%2Fdata-sets&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C041d95ebd14c4d74a35b08dc6ad7c2fd%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638502722122927280%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=ZOMkv3C374WwkbTOVhUOsCt6J3AdtFPZKsX9aprONac%3D&reserved=0>
>>>> (Accession Number 001-2017)) as dataset in GDF file, I want to preprocess
>>>> and use ft_definetrial, but it is not accessed to the event code. In this
>>>> regard I use EEGLAB to load the dataset with biosig, after that when I
>>>> convert to fieldtrip (eeglab2fieldtrip or save it and use ft_read_event,..)
>>>> I face this problem as follows. Could you please help me how can I
>>>> preprocess this dataset for beamforming source localization for specific
>>>> event code.
>>>>
>>>> Error using isfolder
>>>> Input path must be text.
>>>>
>>>> Error in ft_filetype (line 166)
>>>> if isfolder(filename)
>>>>
>>>> Error in dataset2files (line 42)
>>>> format = ft_filetype(filename);
>>>>
>>>> Error in ft_checkconfig (line 675)
>>>> [cfg.dataset, cfg.headerfile, cfg.datafile] =
>>>> dataset2files(cfg.dataset, []);
>>>>
>>>> Error in ft_preprocessing (line 385)
>>>> cfg = ft_checkconfig(cfg, 'dataset2files', 'yes');
>>>>
>>>>
>>>> _______________________________________________
>>> fieldtrip mailing list
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C041d95ebd14c4d74a35b08dc6ad7c2fd%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638502722122927280%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=YhPuPSYLY9PdP15Bv%2BN2M31GC0xzH2szXFlAgj85Xtw%3D&reserved=0>
>>> https://doi.org/10.1371/journal.pcbi.1002202
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> https://doi.org/10.1371/journal.pcbi.1002202
>>>
>>
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