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Generic Decoding Demo/Python

This is Python code for Generic Decoding Demo.

Requirements

All scripts are tested with Python 2.7.13. The following packages are required.

  • bdpy
  • numpy
  • scipy
  • pandas
  • scikit-learn
  • matplotlib (mandatory for creating figures)
  • caffe (mandatory if you calculate image and category features by yourself)
  • PIL (mandatory if you calculate image and category features by yourself)

Data organization

All data should be placed in python/data. Data can be obrained from figshare. The data directory should have the following files:

data/ --+-- Subject1.h5 (fMRI data, subject 1)
        |
        +-- Subject2.h5 (fMRI data, subject 2)
        |
        +-- Subject3.h5 (fMRI data, subject 3)
        |
        +-- Subject4.h5 (fMRI data, subject 4)
        |
        +-- Subject5.h5 (fMRI data, subject 5)
        |
        +-- ImageFeatures.h5 (image features extracted with Matconvnet)

Download links:

Script files

  • analysis_FeaturePrediction.py: Run image feature prediction for each subject, ROI, and layer (feature).
  • analysis_FeaturePredictionMergeResults.py: Merge outputs of analysis_FeaturePrediction.py and calculate feature prediction accuracy.
  • analysis_CategoryIdentification.py: Run category identification.
  • createfigure.py: Create result figures.
  • god_config.py: Define analysis parameters. This file is called in analysis_* scripts.

Analysis

Run the following scripts.

$ python analysis_FeaturePrediction.py
$ python analysis_FeaturePredictionMergeResults.py
$ python analysis_CategoryIdentification.py

The all results will be saved in results directory.

To visualize the results, run the following script.

$ python createfigure.py

createfigure.py will create two figures: one shows the results of image feature and category-averaged feature prediction, and the other displays the results of category identification. The figures will be saved in results directory in PDF format (createfigure_featureprediction.pdf and createfigure_categoryidentification.pdf).