├── .gitattributes ├── .github └── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── custom.md │ └── feature_request.md ├── .gitignore ├── BME-X.py ├── BME_X ├── BIDS_data.py ├── BME_X.py ├── BME_X.sh ├── BME_X_enhanced.py ├── Templates │ ├── Template-Fetal-T2w.nii.gz │ ├── Template-Month0-T1w.nii.gz │ ├── Template-Month0-T2w.nii.gz │ ├── Template-Month12-T1w.nii.gz │ ├── Template-Month12-T2w.nii.gz │ ├── Template-Month18-T1w.nii.gz │ ├── Template-Month18-T2w.nii.gz │ ├── Template-Month24-T1w.nii.gz │ ├── Template-Month24-T2w.nii.gz │ ├── Template-Month3-T1w.nii.gz │ ├── Template-Month3-T2w.nii.gz │ ├── Template-Month6-T1w.nii.gz │ ├── Template-Month6-T2w.nii.gz │ ├── Template-Month9-T1w.nii.gz │ └── Template-Month9-T2w.nii.gz ├── checkpoints │ └── README.md ├── models │ ├── DUNet3D_seg_recon_softmax.py │ ├── DenseUNet3d.py │ ├── __init__.py │ ├── base_model.py │ ├── building_blocks │ │ ├── DenseBlock.py │ │ ├── TransitionBlock.py │ │ ├── UpsamplingBlock.py │ │ └── __init__.py │ ├── evaluation │ │ ├── __init__.py │ │ ├── dice_score.py │ │ └── evaluate.py │ ├── models.py │ ├── networks.py │ ├── networks_bk.py │ └── test_model.py ├── options │ ├── __init__.py │ ├── base_options.py │ ├── test_options.py │ └── train_options.py └── util │ ├── __init__.py │ ├── get_data.py │ ├── html.py │ ├── image_pool.py │ ├── png.py │ ├── util.py │ └── visualizer.py ├── CONTRIBUTING.md ├── Caffe_BME_X.py ├── Caffe_BME_X_docker.py ├── Caffe_Templates └── README.md ├── Caffe_pretrained_models ├── README.md ├── deploy.prototxt └── deploy1.prototxt ├── DUNet3D.py ├── DUNet3D_T1w.py ├── DUNet3D_T2w.py ├── Dockerfile ├── For_reference ├── README.txt └── TCT.py ├── Gamma_correction.py ├── LICENSE ├── LifespanStrip-bids-docker.py ├── Model └── README.md ├── PyTorch_version ├── Enhancement_model.py └── README.md ├── README.md ├── Template ├── template.hdr └── template.img ├── Testing_subjects ├── README.md ├── output │ ├── README.txt │ └── test_24m-enhanced.nii.gz └── test_24m.nii.gz ├── Training_files ├── README.md ├── solver.prototxt ├── test_dataset.txt ├── train.prototxt └── train_dataset.txt ├── layers.py ├── networks ├── __init__.py ├── blocks.py └── net.py ├── optimizers ├── __init__.py └── lr_scheduler.py ├── output.log ├── requirements.txt ├── test_BIDS ├── README.md ├── dataset_description.json ├── sub-0001 │ ├── ses-V01 │ │ ├── anat │ │ │ ├── sub-0001_ses-V01_T1w.json │ │ │ ├── sub-0001_ses-V01_T1w.nii.gz │ │ │ └── sub-0001_ses-V01_scans.tsv │ │ ├── sub-0001_ses-V01_scans.json │ │ └── sub-0001_ses-V01_scans.tsv │ ├── ses-V02 │ │ └── anat │ │ │ ├── sub-0001_ses-V02_T1w.json │ │ │ └── sub-0001_ses-V02_T1w.nii.gz │ ├── sub-0001_sessions.json │ └── sub-0001_sessions.tsv ├── sub-0002 │ └── ses-V01 │ │ ├── anat │ │ └── sub-0002_ses-V01_T1w.nii.gz │ │ ├── sub-0002_ses-V01_scans.json │ │ └── sub-0002_ses-V01_scans.tsv ├── sub-0003 │ └── ses-V01 │ │ ├── anat │ │ └── sub-0003_ses-V01_T1w.nii.gz │ │ ├── sub-0003_ses-V01_scans.json │ │ └── sub-0003_ses-V01_scans.tsv ├── sub-0004 │ └── ses-V01 │ │ ├── anat │ │ └── sub-0004_ses-V01_T1w.nii.gz │ │ ├── sub-0004_ses-V01_scans.json │ │ └── sub-0004_ses-V01_scans.tsv ├── sub-0005 │ └── ses-V01 │ │ ├── anat │ │ └── sub-0005_ses-V01_T1w.nii.gz │ │ ├── sub-0005_ses-V01_scans.json │ │ └── sub-0005_ses-V01_scans.tsv ├── sub-0006 │ └── ses-V01 │ │ ├── anat │ │ └── sub-0006_ses-V01_T1w.nii.gz │ │ ├── sub-0006_ses-V01_scans.json │ │ └── sub-0006_ses-V01_scans.tsv ├── sub-0007 │ └── ses-V01 │ │ ├── anat │ │ └── sub-0007_ses-V01_T1w.nii.gz │ │ ├── sub-0007_ses-V01_scans.json │ │ └── sub-0007_ses-V01_scans.tsv ├── sub-0008 │ └── ses-V01 │ │ ├── anat │ │ └── sub-0008_ses-V01_T1w.nii.gz │ │ ├── sub-0008_ses-V01_scans.json │ │ └── sub-0008_ses-V01_scans.tsv └── sub-0009 │ └── ses-V01 │ ├── anat │ ├── sub-0009_ses-V01_T2w.nii.gz │ └── sub-0009_ses-V01_scans.tsv │ ├── sub-0009_ses-V01_scans.json │ └── sub-0009_ses-V01_scans.tsv ├── test_BIDS_raw ├── dataset_description.json └── sub-0001 │ ├── ses-V01 │ ├── anat │ │ ├── sub-0001_ses-V01_T2w.json │ │ ├── sub-0001_ses-V01_T2w.nii.gz │ │ └── sub-0001_ses-V01_scans.tsv │ ├── sub-0001_ses-V01_scans.json │ └── sub-0001_ses-V01_scans.tsv │ ├── sub-0001_sessions.json │ └── sub-0001_sessions.tsv ├── test_BIDS_withBrainMask ├── dataset_description.json └── sub-0001 │ ├── ses-V01 │ ├── anat │ │ ├── sub-0001_ses-V01_T2w-brainmask.nii.gz │ │ ├── sub-0001_ses-V01_T2w.json │ │ ├── sub-0001_ses-V01_T2w.nii.gz │ │ └── sub-0001_ses-V01_scans.tsv │ ├── sub-0001_ses-V01_scans.json │ └── sub-0001_ses-V01_scans.tsv │ ├── sub-0001_sessions.json │ └── sub-0001_sessions.tsv ├── trainer.py └── utils ├── __init__.py ├── bids.py ├── data_utils.py └── utils.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DBC-Lab/Brain_MRI_Enhancement/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: 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