koasis

Keras pre-trained deep neural networks for Open Access Series of Imaging Studies (OASIS) feature extraction.

Getting Started

Dependencies

You need Python 3.7 or later to use koasis. You can find it at python.org.

You aso need numpy, pandas and keras packages, which is available from PyPI. If you have pip, just run:

pip install numpy
pip install pandas
pip install keras

Installation

Clone this repo to your local machine using:

git clone https://github.com/caiocarneloz/keras-oasis.git

Features

With this code, its possible to:

• Retrieve all the labels from clinical info (considering CDR)
• Extract features from any OASIS-1 image using Keras Applications
• Generate a dataset containing all non-zero features and corresponding labels

Usage

Actually, you need to create a folder containing all OASIS images and CDR info. Having this, it is necessary just call the oasis_extract function sending the folder path:

oasis_extract('folder/')

Output

As output, for each pre-trained model, a .csv file containing the features and labels is generated:

            0         1         2    3  ...       6223       6224  6225       6226
0    0.751712  0.000000  4.072742  0.0  ...  42.221912   0.000000   0.0    Control
1    2.542512  0.000000  3.418418  0.0  ...  13.266520   5.047302   0.0    Control
2    0.904695  0.000000  3.447591  0.0  ...   7.464177   0.000000   0.0  Alzheimer
3    1.975773  0.000000  5.956251  0.0  ...  41.108479   0.000000   0.0    Control
4    0.000000  0.000000  0.584957  0.0  ...   2.805410   4.802437   0.0    Control
5    1.465851  0.000000  5.688468  0.0  ...  53.284348   0.000000   0.0    Control
6    0.000000  0.000000  6.295202  0.0  ...  20.517311   0.000000   0.0    Control
7    0.565955  0.000000  5.364164  0.0  ...  29.104387   0.000000   0.0    Control
8    2.452629  0.000000  3.623104  0.0  ...   8.846025   5.419124   0.0    Control
9    1.460919  0.000000  2.128028  0.0  ...  43.439747   0.000000   0.0    Control
10   3.632581  0.000000  4.830678  0.0  ...  23.841797  14.104014   0.0    Control
11   3.157856  0.000000  4.083702  0.0  ...  17.051870   6.060349   0.0  Alzheimer

Citation

If you use OASIS dataset, please cite the original publication:

MARCUS, Daniel S. et al. Open Access Series of Imaging Studies (OASIS): cross-sectional MRI data in young, middle aged, nondemented, and demented older adults. Journal of cognitive neuroscience, v. 19, n. 9, p. 1498-1507, 2007.