Convert BS to filedtrip

tourette95 · June 8, 2020, 9:51pm

Hi everyone!

I would like to export some eeg procesed in BS, to fieldtrip in order to perform further analysis,
I know there are some scripts in order to make it, but I don't really get how to use it,
I would like to process, filter, clean and select epochs with BS, and then export that cleanned file to open it with fieldtrip,

A tutorial about converting BS to fieldtrip structures (step guided) could be great!!

Thanks in advance!

Francois · June 9, 2020, 8:33am

All the functions to convert from Brainstorm structures to FieldTrip structures are named out_fieldtrip_*.m.
Read the header of the functions for help.
If you are familiar with data structures and scripting in Brainstorm, it should be self-explanatory. If you are not, read this tutorial first (the section "File structures" lists links to the description of all the Brainstorm data structures):
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting

You can find examples of how to call these functions in the FieldTrip-based processes: process_ft_*.m

tourette95 · June 9, 2020, 3:21pm

Thanks!
it seems easy, but it also seems like that will only work on continous or not database imported data, the data I would like to convert to Fieldtrip is epoched (once data is clean and I selected "import to database" option from the raw file).
Can it be done?
Thanks in advance!

ps: I saw there is also a script to convert BS matrix to Fieldtrip, will it work with a connectivity matrix, To analyse results from computing coherence with BS, in Fieldtrip?

Francois · June 10, 2020, 8:24am

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/out_fieldtrip_data.m

function [ftData, DataMat, ChannelMat, iChannels] = out_fieldtrip_data( DataFile, ChannelFile, SensorTypes, isTimelock )
% OUT_FIELDTRIP_DATA: Converts a data file into a FieldTrip structure (ft_datatype_timelock.m / ft_datatype_raw.m)
% 
% USAGE:  [ftData, DataMat, ChannelMat, iChannels] = out_fieldtrip_data( DataFile, ChannelFile=[], SensorTypes/iChannels=[], isTimelock=0 );
%         [ftData, DataMat, ChannelMat, iChannels] = out_fieldtrip_data( DataMat,  ChannelMat=[],  SensorTypes/iChannels=[], isTimelock=0 );
%
% INPUTS:
%    - DataFile     : Relative path to a recordings file available in the database
%    - DataMat      : Brainstorm data file structure
%    - ChannelFile  : Relative path to a channel file available in the database (if not provided: look for it based on the DataFile)
%    - ChannelMat   : Brainstorm channel file structure
%    - iChannels    : Vector of selected channel indices
%    - SensorTypes  : Names or types of channels, separated with commas
%    - isTimelock   : If 1, return a FieldTrip structure "timelock"  (see ft_datatype_timelock.m)
%                     If 0, return a FieldTrip structure "raw"       (see ft_datatype_raw.m)

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
%

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github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/out_fieldtrip_channel.m

function [elec, grad] = out_fieldtrip_channel(ChannelFile, isIncludeRef)
% OUT_FIELDTRIP_CHANNEL: Converts a channel file into elec/grad structures
% 
% USAGE:  [elec, grad] = out_fieldtrip_channel(ChannelFile, isIncludeRef=1)
%         [elec, grad] = out_fieldtrip_channel(ChannelMat)

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c)2000-2020 University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
% 
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.

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ps: I saw there is also a script to convert BS matrix to Fieldtrip, will it work with a connectivity matrix, To analyse results from computing coherence with BS, in Fieldtrip?

No, it is not possible to convert automatically connectivity structures (yet).
Three options:

do your connectivity analysis and statics both in Brainstorm
do your connectivity analysis and statics both in FieldTrip
write a short conversion script to create a FieldTrip structure from the Brainstorm results. This is not complicated if you are already familiar with the two environments, and you already have some examples (all the out_fieldtrip_*.m functions)

tourette95 · June 13, 2020, 12:08am

I see!
Thank you

kkauraiims · May 31, 2022, 9:29pm

Hi Francois! I am trying to use this code to export a brainstorm preprocessed recording to Fieldtrip. However, I am getting the error messages attached in the screenshot.

The following is the code I used for specifying input files:

[ftData, DataMat, ChannelMat, iChannels] = out_fieldtrip_data ('A4/@rawA4_2_281214-1_tsss_mc_resample_notch_band/brainstormstudy.mat', 'A4/data/A4/@rawA4_2_281214-1_tsss_mc/channel_vectorview306_acc1.mat', 'MEG', 0 );

Can you indicate where I may be going wrong?

Thanks for your help as always!

Francois · June 1, 2022, 4:24pm

The first parameter of out_fieldtrip_data must be the file containing the recordings or a "Link to raw file", starting with the tag data_. Instead, you selected the file brainstormstudy.mat, which only contains a few metadata related with the folder.

Some examples here: Tutorials/Scripting - Brainstorm

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/out_fieldtrip_data.m

function [ftData, DataMat, ChannelMat, iChannels] = out_fieldtrip_data( DataFile, ChannelFile, SensorTypes, isTimelock )
% OUT_FIELDTRIP_DATA: Converts a data file into a FieldTrip structure (ft_datatype_timelock.m / ft_datatype_raw.m)
% 
% USAGE:  [ftData, DataMat, ChannelMat, iChannels] = out_fieldtrip_data( DataFile, ChannelFile=[], SensorTypes/iChannels=[], isTimelock=0 );
%         [ftData, DataMat, ChannelMat, iChannels] = out_fieldtrip_data( DataMat,  ChannelMat=[],  SensorTypes/iChannels=[], isTimelock=0 );
%
% INPUTS:
%    - DataFile     : Relative path to a recordings file available in the database
%    - DataMat      : Brainstorm data file structure
%    - ChannelFile  : Relative path to a channel file available in the database (if not provided: look for it based on the DataFile)
%    - ChannelMat   : Brainstorm channel file structure
%    - iChannels    : Vector of selected channel indices
%    - SensorTypes  : Names or types of channels, separated with commas
%    - isTimelock   : If 1, return a FieldTrip structure "timelock"  (see ft_datatype_timelock.m)
%                     If 0, return a FieldTrip structure "raw"       (see ft_datatype_raw.m)

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
%

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Daimenga426 · September 17, 2023, 9:18am

Hi Francois! I am trying to use this code. I selected the file data_0raw_SZ089_HF_20230524_01_notch_band.mat, but it maybe something is wrong.

[ftData, DataMat, ChannelMat, iChannels] = out_fieldtrip_data('D:\F\brainstrom\brainstorm_db\Protocol01\data\hc005@rawSZ088_HF_20230524_05_notch_band\data_0raw_SZ088_HF_20230524_05_notch_band.mat', 'D:\F\brainstrom\brainstorm_db\Protocol01\data\hc005@rawSZ088_HF_20230524_05_notch_band\channel_ctf_acc1.mat', 'MEG','0');
位置 1 的索引超出数组范围(不能超过 1)。

出错 out_fieldtrip_data (line 100)
ftData.avg = DataMat.F(iChannels,:);

How should I modify them?

Raymundo.Cassani · September 18, 2023, 1:55pm

Hi @Daimenga426, the export of raw files was not fully implemented.
Now it is: commit be9102b

Please update your Brainstorm instance and try again