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Process: Run Matlab command If you want to modify the values saved in a file eg. It is also available from Process2 in the category "Other". It loads the files in input and run them through a piece of Matlab code that you can edit freely. It can extend a lot the flexibility of the Brainstorm pipeline manager, providing an easy access to any Matlab function or script.

FileName: Absolute path to a. FileMat: Valid Brainstorm structure, corresponding to the file type. Version: Defines which version of the Matlab. This function saves the file and then reloads the folder. FileMat must be a structure, not a filename. You should not save the file manually before calling this function.

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HideEdgeEffects : Controls the checkbox "Hide edge effects" 0 or 1. HighResolution : Controls the checkbox "Smooth display" 0 or 1. RowName : Controls the signal that is currently displayed for 'SingleSensor' display mode. Function : Controls the display function magnitude, power, log, phase. Correction: Correction for multiple comparisons 'none', 'fdr', 'bonferroni' StatThreshOptions.

Example: Creating a new file This section illustrates how to add new files to the database. We will create a sinusoidal signal and save it in a "matrix" file, in a new folder of the subject "Test". For example, we have to combine external triggers or behavioral information with the existing events. This example illustrates how to load the events, modify them and save them back. For the continuous recordings, the events are saved in the. First, we need to load this link. We need first to identify what is the index of the category "button" , in this array of 7 event structures.

The final call to the find function returns at which indices the list of tags found in the event label is not empty. If you add or remove events, you must adjust the size of the other fields: epochs always 1 for most file formats , channels and notes cell array of empty matrices in most cases. Find examples in the code The easier way to understand how to use a function is to search the code with the " Find files " interface in Matlab.

It will return all the lines that include the string you entered across all the files in the Brainstorm distribution. Just double-click on a line to jump to the code in the Matlab editor. You can use the same interface to find what function is called when you click on a button or menu in the interface. Search for the label or the tooltip of the interface element in the same way. The example below shows how to track what happens when you click on the headmodel popup menu "Check spheres". If you have trouble understanding how to set some input parameters, you can use the debugger to explore a real use case.

Then click on the corresponding menus in the Brainstorm interface eg. When the execution reaches the line you selected, it stops and gives you back the commands.

You can explore the values in all the variables, modify them, and execute the code step by step many options available in the Editor tab of Matlab. Additional quality control You can add in the reports all the information that may help you control the quality of the analysis, or figures you want to include in publications or clinical reports.

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The example below shows how to add a " raster plot " for all the deviant trials from Run 01 in the report. The example below shows how to create a loop over subjects to import their anatomy. The dataset used here is from the tutorial MEG visual: single subject. It contains the same steps of analysis as the introduction tutorials, but separating what can be done automatically from what should be done manually.

This workflow can be adapted to most ERP studies stimulus-based. Prototype : Start by processing one or two subjects completely interactively exactly like in the introduction tutorials. Use the few pilot subjects that you have for your study to prototype the analysis pipeline and check manually all the intermediate stages.

Take notes of what you're doing along the way, so that you can later write a script that reproduces the same operations.

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You will not have to redo this even if you have to start over your analysis from the beginning. Script : Write a loop that calls the process "Import anatomy folder" for all the subjects. Alternatives : Create and import the subjects one by one and set the fiducials at the import time. Or use the default anatomy for all the subjects or use warped templates.

Script 1 : Pre-processing: Loop on the subjects and the acquisition runs. Create link to raw files : Link the subject and noise recordings to the database.

Event markers : Read and group triggers from digital and analog channel, fix stimulation delays Evaluation : Power spectrum density of the recordings to evaluate their quality. Pre-processing : Notch filter, sinusoid removal, band-pass filter. Evaluation : Power spectrum density of the recordings to make sure the filters worked well. Cleanup : Delete the links to the original files the filtered ones are copied in the database.

Detect artifacts : Detect heartbeats, Detect eye blinks, Remove simultaneous. Manual inspection 1 : Check the reports : Information messages number of events, errors and warnings and screen captures registration problems, obvious noisy channels, incorrect SSP topographies.


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Mark bad channels : Open the recordings, select the channels and mark them as bad. Or use the process "Set bad channels" to mark the same bad channels in multiple files. Detect other artifacts : Run the process on all the runs of all the subjects at once select all the files in Process1 and run the process, or generate the equivalent script.

Mark bad segments : Review the artifacts detected in Hz and Hz, keep only the ones you really want to remove, then mark the event categories as bad. Review quickly the rest of the file and check that there are no other important artifacts. Script 2 : Subject-level analysis: Epoching, averaging, sources, time-frequency.

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Averaging : Average trials by run, average runs by subject registration problem in MEG. Noise covariance : Compute from empty room or resting recordings, copy to other folders. Head model : Compute for each run, or compute once and copy if the runs are co-registered. Sources : Compute for each run, average across runs and subjects in source space for MEG. Time-frequency : Computation with Hilbert transform or Morlet wavelets, then normalize.

Screenshots : Check the quality of all the averages time series, topographies, sources. Manual inspection 2 : Check the reports : Check the number of epochs imported and averaged in each condition, check the screen capture of the averages all the primary responses should be clearly visible. Regions of interest : If not using predefined regions from an atlas, define the scouts on the anatomy of each subject or on the template and then project them to the subjects. Script 3 : Group analysis, ROI-based analysis, etc. Averaging : Group averages for the sensor data, the sources and the time-frequency maps.