How to save Time Frequency plot in to image generated from Brainstorm software?

manojec111 · February 28, 2020, 6:29am

I am working in the Brainstorm Software for EEG signal processing and try to extract the Time-frequency. That was extracted through the pipeline editor.

The problem is that how can I directly get the Time-Frequency in image form the brainstorm to Matlab or Can be saved in the .jpg/.png format in local derive.

Can It be done through programmatically? So, that I can save lot of time by doing that manually?

Help me as soon as possible.

Thank you in advance.

Francois · February 28, 2020, 3:26pm

You can open the file with view_timefreq, then configure it with functions in panel_display.m or figure_timefreq.m. Set it to the appropriate size (change the "Position" property of the Matlab figure handle).

Then take a screen capture with one the following functions:

print('test.jpg', '-djpeg', hFig)
saveas(hFig, 'test', 'jpg')
out_figure_image(hFig, 'test.jpg')
take a screen capture in a report with process "File > Snapshot" then save all the images in the report with the button "Export" and file format "PNG images"
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Starting_a_new_script
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Line_by_line:_Footer
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Additional_quality_control

manojec111 · February 29, 2020, 11:00am

Could you send me some links to the steps for saving the Time-Frequency in *.png/jpg format for a bunch of files ? Interactively or using the script.

I don't know about how to view the TF in " open the file with view_timefreq".
I have attached the screenshot too.
Help me, Francois thanks for a quick reply.

Francois · March 1, 2020, 11:25am

Read the help directly in the header of the function view_timefreq.m

If you are trying to do some advanced scripting with Brainstorm, start by reading this tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting

You can find examples of a script using this function in this tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Final_scripts

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/script/tutorial_introduction.m#L967


sEpochsAvgTf = bst_process('CallProcess', 'process_timefreq', sFilesEpochs1, [], ...

    'sensortypes', 'MEG, EEG', ...

    'edit',        TfOptions, ...

    'normalize',   'none');  % None: Save non-standardized time-frequency maps

% Process: Event-related perturbation (ERS/ERD): [-75ms,0ms]

sEpochsAvgTfErsd = bst_process('CallProcess', 'process_baseline_norm', sEpochsAvgTf, [], ...

    'baseline',  [-0.075, 0], ...

    'method',    'ersd', ...  % Event-related perturbation (ERS/ERD):    x_std = (x - &mu;) / &mu; * 100

    'overwrite', 0);



% === DISPLAY ===

% View time-frequency file

hFigTf1 = view_timefreq(sEpochsAvgTfErsd.FileName, 'SingleSensor');

% Configure display

sOptions = panel_display('GetDisplayOptions');

sOptions.HideEdgeEffects = 1;

sOptions.HighResolution = 1;

panel_display('SetDisplayOptions', sOptions);

% Other display modes

hFigTf2 = view_timefreq(sEpochsAvgTfErsd.FileName, 'AllSensors');

hFigTf3 = view_timefreq(sEpochsAvgTfErsd.FileName, '2DLayout');