├── .gitattributes ├── .github └── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── ICA-AROMA ├── .gitignore ├── Dockerfile ├── ICA_AROMA.py ├── ICA_AROMA_functions.py ├── Manual.pdf ├── README.md ├── classification_plots.py ├── ica-aroma-via-docker.py ├── license.md ├── mask_csf.nii.gz ├── mask_edge.nii.gz ├── mask_out.nii.gz └── requirements.txt ├── LICENSE ├── README.md ├── figures ├── autoencoder phase 1.jpg ├── autoencoder phase 2.jpg ├── autoencoder phase 3.jpg ├── autoencoder phase 4.jpg ├── fMRI protocol.jpg ├── highpass_temp.png ├── preprocessing_step_1.png ├── registrate funtional scans to sctural scans.png └── vae_model.png ├── sample data ├── FreesurferLTU.csv └── volume_of_interest │ ├── CSI1_session1_run1_volume1.nii.gz │ ├── CSI1_session1_run1_volume10.nii.gz │ ├── CSI1_session1_run1_volume11.nii.gz │ ├── CSI1_session1_run1_volume12.nii.gz │ ├── CSI1_session1_run1_volume13.nii.gz │ ├── CSI1_session1_run1_volume14.nii.gz │ ├── CSI1_session1_run1_volume15.nii.gz │ ├── CSI1_session1_run1_volume16.nii.gz │ ├── CSI1_session1_run1_volume17.nii.gz │ ├── CSI1_session1_run1_volume18.nii.gz │ ├── CSI1_session1_run1_volume19.nii.gz │ ├── CSI1_session1_run1_volume2.nii.gz │ ├── CSI1_session1_run1_volume20.nii.gz │ ├── CSI1_session1_run1_volume21.nii.gz │ ├── CSI1_session1_run1_volume22.nii.gz │ ├── CSI1_session1_run1_volume23.nii.gz │ ├── CSI1_session1_run1_volume24.nii.gz │ ├── CSI1_session1_run1_volume25.nii.gz │ ├── CSI1_session1_run1_volume26.nii.gz │ ├── CSI1_session1_run1_volume27.nii.gz │ ├── CSI1_session1_run1_volume28.nii.gz │ ├── CSI1_session1_run1_volume29.nii.gz │ ├── CSI1_session1_run1_volume3.nii.gz │ ├── CSI1_session1_run1_volume30.nii.gz │ ├── CSI1_session1_run1_volume4.nii.gz │ ├── CSI1_session1_run1_volume5.nii.gz │ ├── CSI1_session1_run1_volume6.nii.gz │ ├── CSI1_session1_run1_volume7.nii.gz │ ├── CSI1_session1_run1_volume8.nii.gz │ └── CSI1_session1_run1_volume9.nii.gz └── scripts ├── 0.1.unzip files.py ├── 0.2.MRIconvert.py ├── 1.1.fmri_preprocessing.py ├── 1.2.ICA AROMA.py ├── 1.4.high pass filter.py ├── 1.5.convert image dimension and voxel size.py ├── 2.1.split data into train and validation.py ├── 2.2.extract volumes.py ├── 3.1.simple autoencoder 2D.py ├── old codes ├── 3.1.simple autoencoder 2D.py ├── 3.2.simple autoencoder 3D.py ├── simple autoencoder 2D with pretrained models (part 1 - extract latent representations).py ├── simple autoencoder 2D with pretrained models (part 2 - train only the decoder first).py ├── simple autoencoder 2D with pretrained models.py ├── simple autoencoder 2D.py └── simple autoencoder 3D.py ├── search for BET parameters for T1 scans.py ├── utils.py └── utils_deep.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nmningmei/BOLD5000_autoencoder/HEAD/.gitattributes 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