Beauchamp:RAVE:Data Formats

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Beauchamp Lab



R Analysis and Visualization of ECOG Data (RAVE)

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Getting your data into RAVE

  1. The general folder structure is RAVE_raw_dir/subject_code/block_number/*.mat.
    1. For instance, /Volumes/data/rave_data/raw/NAA/001/, /Volumes/data/rave_data/raw/NAA/002/ and /Volumes/data/rave_data/raw/NAA/003/ contain the data for blocks 001 through 003 for subject NAA. The RAVE raw dir is located at /Volumes/data/rave_data/raw
  2. RAVE requires one .mat file per electrode. Inside this .mat file is a variable with the EEG voltage data. The name of the variable should be analogTraces
  3. The naming of each channel follows a strict pattern. For example: NAADatafile003_ch1.mat means subject NAA, block 003 (the leading 0 are important) and channel 1.
  4. When you run RAVE pre-process application (rave_preprocess()), the program requires you first input the subject code and project name.
  5. Press Create Subject after inputting the Subject Code and Project Name and the application will create a subject directory in your RAE_data_dir/ProjectName folder and then scan your RAVE_raw_dir to look for available blocks.
  6. The user then selects the blocks that go with the particular experiment (using a multi-selector).
  7. After selecting the blocks, input the electrodes (a range may be specified) and the sampling rate (in Hz, must be the same for all channels across all blocks)
  8. Press the "Import Subject" button to import the raw data into that subject's directory in your RAVE_data_dir/ProjectName.

[Deprecated] Older method for formatting data for RAVE

  1. Assume you have pre-processed your subject and have 1 mat file per electrode
    • Pre-processing pipeline in our data includes common average reference, epoching, notch filtering, time-frequency analysis using 'multitaper method' (dpss for 30-200 Hz, hanning for 2-30 Hz), resulting in power-spectra over time at each frequency
    • Each mat file contains a matrix with: [trial, freq, time]
    • these mat files are the output of matlab script 'write_out_electrodes.m'
      • note that since preprocessing at low and high frequencies is performed using different tapers, the 'write_out_electrodes.m' script must concatenate 2-30 Hz with 32-200 Hz data prior to creating mat files
  2. Also need information about each dimension in meta folder
    • 'trials.csv:' data corresponds to the 1st mode in the .mat file.
      • Column 1: Number (numeric) -- cell A1 is 'Number', A2 reads '1', A3 reads '2', ... , An reads 'n'
      • Column 2: Type (string) -- cell B1 reads 'Type', then data begins in B2
      • Column 3: Stimulus (string) -- cell C1 reads 'Stimulus', then data begins in C2
      • Other columns will be imported as a string and made available to the module
      • Note in rAFE GUI, conditions will appear as 'Stimulus_Type'
    • 'frequencies.csv:' has the frequencies that correspond to the 2nd mode in the .mat file
      • Column 1: Frequency (numeric) -- cell A1 reads 'Frequency', then data begins in A2
    • 'time_points.csv:' has the timestamps that correspond to the 3rd mode in the .mat file
      • Column 1: Time (numeric) -- cell A1 reads 'Time'
        • By default, many modules consider values prior to time '0' as the baseline period. In many modules this can also be changed.
    • 'electrodes.csv:' Contains information corresponding to each electrode. In RAFE, this corresponds to the 4th mode of the data, but this is not directly represented in users' the file system.
      • Column 1: Label (string) (this is used throughout the application as a unique identifier)
      • Column 2: Number (integer)
        • This value is not explicitly used in the module, but is required here to facilitate matching with the raw data.
      • Column 3: Valid (0 or 1)
        • If the value is 0, the electrode is not imported into RAFE, or cached, or even checked for existence in the data/ directory. We allow for invalid electrodes to provide a way to match between the raw data files coming from the recording system and the final data that will be analyzed.
      • Column 4-6: Coordinates for the electrode in the space of the surface file
        • Coord_x (numeric)
        • Coord_y (numeric)
        • Coord_z (numeric)
  3. Create a folder in your RAFE data directory (you will tell the application where your data are located, so this location can be arbitrary).
data/
subject_name/
ecog/
e1.mat
...
eN.mat
meta/
trials.csv
frequencies.csv
time_points.csv
electrodes.csv
suma/

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