Extracting scouts for ITPC and PSD + how to do nondeprecated PCA now

Discussions
1

Hi, I analsying already epoched around 3 sec data coming from MEG ASSR experimented;
I am computing ITPC and PSD on the extracted time series
Is this setting sensible settings

% Process: Compute sources [2018]
                sFiles = bst_process('CallProcess', 'process_inverse_2018', sFiles, [], ...
                    'output',  1, ...  % Kernel only: shared
                    'inverse', struct(...
                         'Comment',        'MN: MEG', ...
                         'InverseMethod',  'minnorm', ...
                         'InverseMeasure', 'amplitude', ...
                         'SourceOrient',   {{'fixed'}}, ...
                         'Loose',          0.2, ...
                         'UseDepth',       1, ...
                         'WeightExp',      0.5, ...
                         'WeightLimit',    10, ...
                         'NoiseMethod',    'reg', ...
                         'NoiseReg',       0.1, ...
                         'SnrMethod',      'fixed', ...
                         'SnrRms',         1e-06, ...
                         'SnrFixed',       3, ...
                         'ComputeKernel',  1, ...
                         'DataTypes',      {{'MEG'}}));

                % Process: Scouts time series
                sFiles = bst_process('CallProcess', 'process_extract_scout', sFiles, [], ...
                    'timewindow',     [], ...
                    'scouts',   {'Destrieux', {'G_temp_sup-G_T_transv L', 'G_temp_sup-G_T_transv R', 'G_front_inf-Opercular L', 'G_precentral L'}}, ...
                    'scoutfunc',      1, ...  % Takes the mean of the parce time series
                    'isflip',         0, ...  % If 1, flips the sign of the signals so to avoid cancellation
                    'isnorm',         0, ...
                    'concatenate',    0, ...
                    'save',           1, ...
                    'addrowcomment',  1, ...
                    'addfilecomment', 1);

Also how to do PCA instead of mean extraction now?
If I choose 'scoutfunc', 3, I am receiving error about deprecation and advice to do analysis differently
The tuturial is here https://neuroimage.usc.edu/brainstorm/Tutorials/PCA
but how to use it as a script? (To include it to my current analysis by saving clicked gui step sas a script and then copy is much harder for me than just looking into tutorial and copy additional step to my existing pipeline which is mix of matlab and brainstorm)

2

That's indeed how to do it. You don't need to recreate the whole script through the GUI, just put one result file in the process box, select the extract scout process with the new PCA options you want and export as script. It will show you the options to copy paste into your existing script - just a few lines.

Cheers,
Marc

1 Like