Upload 12 files
Browse files- .gitattributes +6 -0
- manual_annotated/config.json +80 -0
- manual_annotated/model.pt +3 -0
- manual_annotated_synthetic/config.json +80 -0
- manual_annotated_synthetic/model.pt +3 -0
- splits/test_data.nii +3 -0
- splits/test_label.nii +3 -0
- splits/train_data.nii +3 -0
- splits/train_label.nii +3 -0
- splits/val_data.nii +3 -0
- splits/val_label.nii +3 -0
- synthetic/config.json +80 -0
- synthetic/model.pt +3 -0
.gitattributes
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@@ -33,3 +33,9 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.zst filter=lfs diff=lfs merge=lfs -text
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*tfevents* filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.zst filter=lfs diff=lfs merge=lfs -text
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*tfevents* filter=lfs diff=lfs merge=lfs -text
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splits/test_data.nii filter=lfs diff=lfs merge=lfs -text
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splits/test_label.nii filter=lfs diff=lfs merge=lfs -text
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splits/train_data.nii filter=lfs diff=lfs merge=lfs -text
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splits/train_label.nii filter=lfs diff=lfs merge=lfs -text
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splits/val_data.nii filter=lfs diff=lfs merge=lfs -text
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splits/val_label.nii filter=lfs diff=lfs merge=lfs -text
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manual_annotated/config.json
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{
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"batch_size": 32,
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"sliding_window_mode": "constant",
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"models": {
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"lr": "1e-5",
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"wd": 0,
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"activation": "LEAKYRELU",
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"normalization": "BATCH"
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}
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"augmentation": {
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"use_augmentation": true,
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"p_gaussian_noise": 0.5,
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"p_gaussian_smooth": 0.5,
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"p_intensity_scale": 0,
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"p_intensity_shift": 0,
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"p_adjust_contrast": 0,
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"p_histogram_shift": 0.5,
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"p_rotate": 0.5,
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"gaussian_noise_mean": 0.0,
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"gaussian_noise_std": 0.01,
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"gaussian_smooth_sigma": [
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"intensity_scale_factors": [
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"intensity_shift_offsets": [
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"control_points": [
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"rotation": [
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]
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}
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}
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manual_annotated/model.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:4096cd6fc6b8339cb21c2862420cd8ba0e3242f275e8c26bce63b88684e153bf
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size 23320705
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manual_annotated_synthetic/config.json
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{
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"batch_size": 32,
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"sliding_window_mode": "constant",
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"models": {
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"lr": "1e-5",
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"wd": 0,
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"dropout": 0.0,
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"model": "unet",
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"unet": {
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"channels": [
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"strides": [
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],
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"activation": "LEAKYRELU",
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"normalization": "BATCH"
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}
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},
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"augmentation": {
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"patch_size": [
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"use_augmentation": true,
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"p_gaussian_noise": 0.5,
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"p_gaussian_smooth": 0.5,
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"p_intensity_scale": 0,
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"p_intensity_shift": 0,
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"gaussian_noise_mean": 0.0,
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"intensity_scale_factors": [
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"intensity_shift_offsets": [
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"adjust_contrast_gamma": [
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"control_points": [
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"rotation": [
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]
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}
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}
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manual_annotated_synthetic/model.pt
ADDED
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version https://git-lfs.github.com/spec/v1
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size 23320705
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splits/test_data.nii
ADDED
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version https://git-lfs.github.com/spec/v1
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size 6553952
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splits/test_label.nii
ADDED
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version https://git-lfs.github.com/spec/v1
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splits/train_data.nii
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version https://git-lfs.github.com/spec/v1
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size 16384352
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splits/train_label.nii
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version https://git-lfs.github.com/spec/v1
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size 32768352
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splits/val_data.nii
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version https://git-lfs.github.com/spec/v1
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oid sha256:16f21a32ddc84683d69949c1fbed4fc8f3cdd181100089fcdc23def4881ed341
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size 6553952
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splits/val_label.nii
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version https://git-lfs.github.com/spec/v1
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size 13107552
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synthetic/config.json
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{
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"batch_size": 32,
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"sliding_window_mode": "constant",
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"models": {
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"lr": "1e-5",
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"wd": 0,
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"dropout": 0.0,
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"model": "unet",
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"unet": {
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"channels": [
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"strides": [
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],
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"activation": "LEAKYRELU",
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"normalization": "BATCH"
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}
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},
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"augmentation": {
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"patch_size": [
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64,
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"use_augmentation": true,
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"p_gaussian_noise": 0.5,
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"p_gaussian_smooth": 0.5,
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"p_intensity_scale": 0,
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"intensity_scale_factors": [
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]
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}
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}
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synthetic/model.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:db58216635fd02cf1b741e702a20cc7ee344bf933e52ae3e1ad74dbf0821094d
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size 23320705
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