Hugging Face's logo

Spaces:
anirudh0410
/
Prostate-Inference
Sleeping

App Files Community
Anirudh Balaraman commited on
Commit
a1cc9d3
·
1 Parent(s): 3009fda

update psa model

Browse files
Files changed (19) hide show
  1. config/config_cspca_test.yaml +2 -2
  2. config/config_cspca_train.yaml +1 -1
  3. config/config_pirads_test.yaml +1 -1
  4. dataset/PICAI_cspca_updated_with_psa.json +0 -0
  5. dataset/adc_reference.nrrd +0 -3
  6. dataset/dwi_reference.nrrd +0 -3
  7. dataset/prostate_segmentation_reference.nrrd +0 -3
  8. dataset/t2_reference.nrrd +0 -3
  9. dataset/test_data_updated_with_psa.json +802 -0
  10. job_scripts/{train_cspca_2.sh → test_cspca.sh} +2 -2
  11. job_scripts/train_cspca.sh +2 -2
  12. run_cspca.py +11 -0
  13. run_inference.py +2 -0
  14. run_pirads.py +1 -0
  15. src/data/custom_transforms.py +19 -0
  16. src/data/data_loader.py +126 -85
  17. src/model/cspca_model.py +14 -2
  18. src/train/train_cspca.py +4 -2
  19. temp_2.ipynb +0 -0
config/config_cspca_test.yaml CHANGED
@@ -1,5 +1,5 @@
1
  data_root: /sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/t2_registered
2
- dataset_json: /sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/dataset/test_data_updated.json
3
  num_classes: !!int 4
4
  mil_mode: att_trans
5
  tile_count: !!int 40
@@ -7,7 +7,7 @@ tile_size: !!int 48
7
  depth: !!int 3
8
  use_heatmap: !!bool True
9
  workers: !!int 2
10
- checkpoint_cspca: /sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/logs/cspca_train_new/models/cspca_model_20.pth
11
  batch_size: !!int 8
12
 
13
 
 
1
  data_root: /sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/t2_registered
2
+ dataset_json: /sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/dataset/test_data_updated_with_psa.json
3
  num_classes: !!int 4
4
  mil_mode: att_trans
5
  tile_count: !!int 40
 
7
  depth: !!int 3
8
  use_heatmap: !!bool True
9
  workers: !!int 2
10
+ checkpoint_cspca: /sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/logs/cspca_train_psa/models/cspca_model_57.pth
11
  batch_size: !!int 8
12
 
13
 
config/config_cspca_train.yaml CHANGED
@@ -1,5 +1,5 @@
1
  data_root: /sc-projects/sc-proj-cc06-ag-ki-radiologie/pirad_model_test_PICAI/processed/t2_registered/
2
- dataset_json: /sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/dataset/PICAI_cspca_updated.json
3
  mil_mode: att_trans
4
  tile_count: !!int 40
5
  tile_size: !!int 48
 
1
  data_root: /sc-projects/sc-proj-cc06-ag-ki-radiologie/pirad_model_test_PICAI/processed/t2_registered/
2
+ dataset_json: /sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/dataset/PICAI_cspca_updated_with_psa.json
3
  mil_mode: att_trans
4
  tile_count: !!int 40
5
  tile_size: !!int 48
config/config_pirads_test.yaml CHANGED
@@ -1,6 +1,6 @@
1
  run_name: pirads_test_run
2
  data_root: /sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/t2_registered
3
- dataset_json: /sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/dataset/test_data_updated.json
4
  num_classes: !!int 4
5
  mil_mode: att_trans
6
  tile_count: !!int 40
 
1
  run_name: pirads_test_run
2
  data_root: /sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/t2_registered
3
+ dataset_json: /sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate/dataset/test_data_updated_with_psa.json
4
  num_classes: !!int 4
5
  mil_mode: att_trans
6
  tile_count: !!int 40
dataset/PICAI_cspca_updated_with_psa.json ADDED
The diff for this file is too large to render. See raw diff
 
dataset/adc_reference.nrrd DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:46821ddb4373198d98b5877ec69a702718702cbaae6b9ef00b6b5ad235cf3f3e
3
- size 3815961
 
 
 
 
dataset/dwi_reference.nrrd DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:a964835a0c8c016b162a2eaa56456f9704290b3a4128aafeb9b01805166ca7b9
3
- size 3815961
 
 
 
 
dataset/prostate_segmentation_reference.nrrd DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:95984795649662ae405077d334744ac2e9d9fb8db7864c4ea99791a706ccee19
3
- size 13434
 
 
 
 
dataset/t2_reference.nrrd DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:561af922d7461870fcc1e84134d659f7611a8ae73d1a0681fde79808f1cd99a9
3
- size 3815961
 
 
 
 
dataset/test_data_updated_with_psa.json ADDED
@@ -0,0 +1,802 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "test": [
3
+ {
4
+ "image": "0040.nrrd",
5
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0040.nrrd",
6
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0040.nrrd",
7
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0040.nrrd",
8
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0040.nrrd",
9
+ "label": 1.0,
10
+ "pirads": 4.0,
11
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0040.nrrd",
12
+ "psa": [
13
+ 6.5,
14
+ 78.0
15
+ ]
16
+ },
17
+ {
18
+ "image": "0013.nrrd",
19
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0013.nrrd",
20
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0013.nrrd",
21
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0013.nrrd",
22
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0013.nrrd",
23
+ "label": 1.0,
24
+ "pirads": 4.0,
25
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0013.nrrd",
26
+ "psa": [
27
+ 5.9,
28
+ 20.0
29
+ ]
30
+ },
31
+ {
32
+ "image": "0059.nrrd",
33
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0059.nrrd",
34
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0059.nrrd",
35
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0059.nrrd",
36
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0059.nrrd",
37
+ "label": 1.0,
38
+ "pirads": 2.0,
39
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0059.nrrd",
40
+ "psa": [
41
+ 6.0,
42
+ 72.0
43
+ ]
44
+ },
45
+ {
46
+ "image": "0034.nrrd",
47
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0034.nrrd",
48
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0034.nrrd",
49
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0034.nrrd",
50
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0034.nrrd",
51
+ "label": 1.0,
52
+ "pirads": 4.0,
53
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0034.nrrd",
54
+ "psa": [
55
+ 10.4,
56
+ 30.0
57
+ ]
58
+ },
59
+ {
60
+ "image": "0074.nrrd",
61
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0074.nrrd",
62
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0074.nrrd",
63
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0074.nrrd",
64
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0074.nrrd",
65
+ "label": 0.0,
66
+ "pirads": 3.0,
67
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0074.nrrd",
68
+ "psa": [
69
+ 8.37,
70
+ 103.0
71
+ ]
72
+ },
73
+ {
74
+ "image": "0038.nrrd",
75
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0038.nrrd",
76
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0038.nrrd",
77
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0038.nrrd",
78
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0038.nrrd",
79
+ "label": 1.0,
80
+ "pirads": 4.0,
81
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0038.nrrd",
82
+ "psa": [
83
+ 5.06,
84
+ 31.0
85
+ ]
86
+ },
87
+ {
88
+ "image": "0076.nrrd",
89
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0076.nrrd",
90
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0076.nrrd",
91
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0076.nrrd",
92
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0076.nrrd",
93
+ "label": 0.0,
94
+ "pirads": 2.0,
95
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0076.nrrd",
96
+ "psa": [
97
+ 3.98,
98
+ 80.0
99
+ ]
100
+ },
101
+ {
102
+ "image": "0023.nrrd",
103
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0023.nrrd",
104
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0023.nrrd",
105
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0023.nrrd",
106
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0023.nrrd",
107
+ "label": 0.0,
108
+ "pirads": 4.0,
109
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0023.nrrd",
110
+ "psa": [
111
+ 5.3,
112
+ 31.0
113
+ ]
114
+ },
115
+ {
116
+ "image": "0008.nrrd",
117
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0008.nrrd",
118
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0008.nrrd",
119
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0008.nrrd",
120
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0008.nrrd",
121
+ "label": 1.0,
122
+ "pirads": 5.0,
123
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0008.nrrd",
124
+ "psa": [
125
+ 21.0,
126
+ 42.0
127
+ ]
128
+ },
129
+ {
130
+ "image": "0065.nrrd",
131
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0065.nrrd",
132
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0065.nrrd",
133
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0065.nrrd",
134
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0065.nrrd",
135
+ "label": 1.0,
136
+ "pirads": 2.0,
137
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0065.nrrd",
138
+ "psa": [
139
+ 5.3,
140
+ 50.0
141
+ ]
142
+ },
143
+ {
144
+ "image": "0055.nrrd",
145
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0055.nrrd",
146
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0055.nrrd",
147
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0055.nrrd",
148
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0055.nrrd",
149
+ "label": 1.0,
150
+ "pirads": 5.0,
151
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0055.nrrd",
152
+ "psa": [
153
+ 4.6,
154
+ 70.0
155
+ ]
156
+ },
157
+ {
158
+ "image": "0009.nrrd",
159
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0009.nrrd",
160
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0009.nrrd",
161
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0009.nrrd",
162
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0009.nrrd",
163
+ "label": 1.0,
164
+ "pirads": 4.0,
165
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0009.nrrd",
166
+ "psa": [
167
+ 9.95,
168
+ 61.0
169
+ ]
170
+ },
171
+ {
172
+ "image": "0067.nrrd",
173
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0067.nrrd",
174
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0067.nrrd",
175
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0067.nrrd",
176
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0067.nrrd",
177
+ "label": 1.0,
178
+ "pirads": 4.0,
179
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0067.nrrd",
180
+ "psa": [
181
+ 3.8,
182
+ 25.0
183
+ ]
184
+ },
185
+ {
186
+ "image": "0007.nrrd",
187
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0007.nrrd",
188
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0007.nrrd",
189
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0007.nrrd",
190
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0007.nrrd",
191
+ "label": 1.0,
192
+ "pirads": 4.0,
193
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0007.nrrd",
194
+ "psa": [
195
+ 12.31,
196
+ 43.0
197
+ ]
198
+ },
199
+ {
200
+ "image": "0075.nrrd",
201
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0075.nrrd",
202
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0075.nrrd",
203
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0075.nrrd",
204
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0075.nrrd",
205
+ "label": 1.0,
206
+ "pirads": 4.0,
207
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0075.nrrd",
208
+ "psa": [
209
+ 5.6,
210
+ 20.0
211
+ ]
212
+ },
213
+ {
214
+ "image": "0073.nrrd",
215
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0073.nrrd",
216
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0073.nrrd",
217
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0073.nrrd",
218
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0073.nrrd",
219
+ "label": 1.0,
220
+ "pirads": 3.0,
221
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0073.nrrd",
222
+ "psa": [
223
+ 7.3,
224
+ 49.0
225
+ ]
226
+ },
227
+ {
228
+ "image": "0010.nrrd",
229
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0010.nrrd",
230
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0010.nrrd",
231
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0010.nrrd",
232
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0010.nrrd",
233
+ "label": 1.0,
234
+ "pirads": 4.0,
235
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0010.nrrd",
236
+ "psa": [
237
+ 7.3,
238
+ 50.0
239
+ ]
240
+ },
241
+ {
242
+ "image": "0066.nrrd",
243
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0066.nrrd",
244
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0066.nrrd",
245
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0066.nrrd",
246
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0066.nrrd",
247
+ "label": 1.0,
248
+ "pirads": 4.0,
249
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0066.nrrd",
250
+ "psa": [
251
+ 9.0,
252
+ 45.0
253
+ ]
254
+ },
255
+ {
256
+ "image": "0026.nrrd",
257
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0026.nrrd",
258
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0026.nrrd",
259
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0026.nrrd",
260
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0026.nrrd",
261
+ "label": 1.0,
262
+ "pirads": 5.0,
263
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0026.nrrd",
264
+ "psa": [
265
+ 8.12,
266
+ 40.0
267
+ ]
268
+ },
269
+ {
270
+ "image": "0056.nrrd",
271
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0056.nrrd",
272
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0056.nrrd",
273
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0056.nrrd",
274
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0056.nrrd",
275
+ "label": 1.0,
276
+ "pirads": 4.0,
277
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0056.nrrd",
278
+ "psa": [
279
+ 3.26,
280
+ 55.0
281
+ ]
282
+ },
283
+ {
284
+ "image": "0015.nrrd",
285
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0015.nrrd",
286
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0015.nrrd",
287
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0015.nrrd",
288
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0015.nrrd",
289
+ "label": 0.0,
290
+ "pirads": 4.0,
291
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0015.nrrd",
292
+ "psa": [
293
+ 1.25,
294
+ 35.0
295
+ ]
296
+ },
297
+ {
298
+ "image": "0044.nrrd",
299
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0044.nrrd",
300
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0044.nrrd",
301
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0044.nrrd",
302
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0044.nrrd",
303
+ "label": 1.0,
304
+ "pirads": 4.0,
305
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0044.nrrd",
306
+ "psa": [
307
+ 4.12,
308
+ 48.0
309
+ ]
310
+ },
311
+ {
312
+ "image": "0017.nrrd",
313
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0017.nrrd",
314
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0017.nrrd",
315
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0017.nrrd",
316
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0017.nrrd",
317
+ "label": 1.0,
318
+ "pirads": 3.0,
319
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0017.nrrd",
320
+ "psa": [
321
+ 13.0,
322
+ 60.0
323
+ ]
324
+ },
325
+ {
326
+ "image": "0030.nrrd",
327
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0030.nrrd",
328
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0030.nrrd",
329
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0030.nrrd",
330
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0030.nrrd",
331
+ "label": 1.0,
332
+ "pirads": 3.0,
333
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0030.nrrd",
334
+ "psa": [
335
+ 5.99,
336
+ 35.0
337
+ ]
338
+ },
339
+ {
340
+ "image": "0025.nrrd",
341
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0025.nrrd",
342
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0025.nrrd",
343
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0025.nrrd",
344
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0025.nrrd",
345
+ "label": 1.0,
346
+ "pirads": 4.0,
347
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0025.nrrd",
348
+ "psa": [
349
+ 13.5,
350
+ 62.0
351
+ ]
352
+ },
353
+ {
354
+ "image": "0005.nrrd",
355
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0005.nrrd",
356
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0005.nrrd",
357
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0005.nrrd",
358
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0005.nrrd",
359
+ "label": 0.0,
360
+ "pirads": 3.0,
361
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0005.nrrd",
362
+ "psa": [
363
+ 5.47,
364
+ 65.0
365
+ ]
366
+ },
367
+ {
368
+ "image": "0011.nrrd",
369
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0011.nrrd",
370
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0011.nrrd",
371
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0011.nrrd",
372
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0011.nrrd",
373
+ "label": 1.0,
374
+ "pirads": 4.0,
375
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0011.nrrd",
376
+ "psa": [
377
+ 13.0,
378
+ 37.0
379
+ ]
380
+ },
381
+ {
382
+ "image": "0071.nrrd",
383
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0071.nrrd",
384
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0071.nrrd",
385
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0071.nrrd",
386
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0071.nrrd",
387
+ "label": 1.0,
388
+ "pirads": 4.0,
389
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0071.nrrd",
390
+ "psa": [
391
+ 11.2,
392
+ 36.0
393
+ ]
394
+ },
395
+ {
396
+ "image": "0033.nrrd",
397
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0033.nrrd",
398
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0033.nrrd",
399
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0033.nrrd",
400
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0033.nrrd",
401
+ "label": 0.0,
402
+ "pirads": 4.0,
403
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0033.nrrd",
404
+ "psa": [
405
+ 3.0,
406
+ 28.0
407
+ ]
408
+ },
409
+ {
410
+ "image": "0052.nrrd",
411
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0052.nrrd",
412
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0052.nrrd",
413
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0052.nrrd",
414
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0052.nrrd",
415
+ "label": 1.0,
416
+ "pirads": 4.0,
417
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0052.nrrd",
418
+ "psa": [
419
+ 5.27,
420
+ 39.0
421
+ ]
422
+ },
423
+ {
424
+ "image": "0032.nrrd",
425
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0032.nrrd",
426
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0032.nrrd",
427
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0032.nrrd",
428
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0032.nrrd",
429
+ "label": 0.0,
430
+ "pirads": 2.0,
431
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0032.nrrd",
432
+ "psa": [
433
+ 13.3,
434
+ 64.0
435
+ ]
436
+ },
437
+ {
438
+ "image": "0035.nrrd",
439
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0035.nrrd",
440
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0035.nrrd",
441
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0035.nrrd",
442
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0035.nrrd",
443
+ "label": 0.0,
444
+ "pirads": 5.0,
445
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0035.nrrd",
446
+ "psa": [
447
+ 6.0,
448
+ 51.0
449
+ ]
450
+ },
451
+ {
452
+ "image": "0039.nrrd",
453
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0039.nrrd",
454
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0039.nrrd",
455
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0039.nrrd",
456
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0039.nrrd",
457
+ "label": 1.0,
458
+ "pirads": 3.0,
459
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0039.nrrd",
460
+ "psa": [
461
+ 7.85,
462
+ 45.0
463
+ ]
464
+ },
465
+ {
466
+ "image": "0079.nrrd",
467
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0079.nrrd",
468
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0079.nrrd",
469
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0079.nrrd",
470
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0079.nrrd",
471
+ "label": 0.0,
472
+ "pirads": 2.0,
473
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0079.nrrd",
474
+ "psa": [
475
+ 4.0,
476
+ 91.0
477
+ ]
478
+ },
479
+ {
480
+ "image": "0054.nrrd",
481
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0054.nrrd",
482
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0054.nrrd",
483
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0054.nrrd",
484
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0054.nrrd",
485
+ "label": 1.0,
486
+ "pirads": 5.0,
487
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0054.nrrd",
488
+ "psa": [
489
+ 8.8,
490
+ 40.0
491
+ ]
492
+ },
493
+ {
494
+ "image": "0031.nrrd",
495
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0031.nrrd",
496
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0031.nrrd",
497
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0031.nrrd",
498
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0031.nrrd",
499
+ "label": 1.0,
500
+ "pirads": 5.0,
501
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0031.nrrd",
502
+ "psa": [
503
+ 18.0,
504
+ 68.0
505
+ ]
506
+ },
507
+ {
508
+ "image": "0053.nrrd",
509
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0053.nrrd",
510
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0053.nrrd",
511
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0053.nrrd",
512
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0053.nrrd",
513
+ "label": 0.0,
514
+ "pirads": 5.0,
515
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0053.nrrd",
516
+ "psa": [
517
+ 29.0,
518
+ 50.0
519
+ ]
520
+ },
521
+ {
522
+ "image": "0012.nrrd",
523
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0012.nrrd",
524
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0012.nrrd",
525
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0012.nrrd",
526
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0012.nrrd",
527
+ "label": 1.0,
528
+ "pirads": 4.0,
529
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0012.nrrd",
530
+ "psa": [
531
+ 7.2,
532
+ 89.0
533
+ ]
534
+ },
535
+ {
536
+ "image": "0050.nrrd",
537
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0050.nrrd",
538
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0050.nrrd",
539
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0050.nrrd",
540
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0050.nrrd",
541
+ "label": 1.0,
542
+ "pirads": 4.0,
543
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0050.nrrd",
544
+ "psa": [
545
+ 9.8,
546
+ 65.0
547
+ ]
548
+ },
549
+ {
550
+ "image": "0082.nrrd",
551
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0082.nrrd",
552
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0082.nrrd",
553
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0082.nrrd",
554
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0082.nrrd",
555
+ "label": 0.0,
556
+ "pirads": 3.0,
557
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0082.nrrd",
558
+ "psa": [
559
+ 5.0,
560
+ 66.0
561
+ ]
562
+ },
563
+ {
564
+ "image": "0058.nrrd",
565
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0058.nrrd",
566
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0058.nrrd",
567
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0058.nrrd",
568
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0058.nrrd",
569
+ "label": 1.0,
570
+ "pirads": 4.0,
571
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0058.nrrd",
572
+ "psa": [
573
+ 7.4,
574
+ 46.0
575
+ ]
576
+ },
577
+ {
578
+ "image": "0049.nrrd",
579
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0049.nrrd",
580
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0049.nrrd",
581
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0049.nrrd",
582
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0049.nrrd",
583
+ "label": 1.0,
584
+ "pirads": 4.0,
585
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0049.nrrd",
586
+ "psa": [
587
+ 4.6,
588
+ 53.0
589
+ ]
590
+ },
591
+ {
592
+ "image": "0077.nrrd",
593
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0077.nrrd",
594
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0077.nrrd",
595
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0077.nrrd",
596
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0077.nrrd",
597
+ "label": 1.0,
598
+ "pirads": 4.0,
599
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0077.nrrd",
600
+ "psa": [
601
+ 3.6,
602
+ 38.0
603
+ ]
604
+ },
605
+ {
606
+ "image": "0021.nrrd",
607
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0021.nrrd",
608
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0021.nrrd",
609
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0021.nrrd",
610
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0021.nrrd",
611
+ "label": 1.0,
612
+ "pirads": 5.0,
613
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0021.nrrd",
614
+ "psa": [
615
+ 15.0,
616
+ 54.0
617
+ ]
618
+ },
619
+ {
620
+ "image": "0080.nrrd",
621
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0080.nrrd",
622
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0080.nrrd",
623
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0080.nrrd",
624
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0080.nrrd",
625
+ "label": 1.0,
626
+ "pirads": 4.0,
627
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0080.nrrd",
628
+ "psa": [
629
+ 15.0,
630
+ 61.0
631
+ ]
632
+ },
633
+ {
634
+ "image": "0006.nrrd",
635
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0006.nrrd",
636
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0006.nrrd",
637
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0006.nrrd",
638
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0006.nrrd",
639
+ "label": 1.0,
640
+ "pirads": 4.0,
641
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0006.nrrd",
642
+ "psa": [
643
+ 6.27,
644
+ 41.0
645
+ ]
646
+ },
647
+ {
648
+ "image": "0036.nrrd",
649
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0036.nrrd",
650
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0036.nrrd",
651
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0036.nrrd",
652
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0036.nrrd",
653
+ "label": 0.0,
654
+ "pirads": 4.0,
655
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0036.nrrd",
656
+ "psa": [
657
+ 7.7,
658
+ 40.0
659
+ ]
660
+ },
661
+ {
662
+ "image": "0001.nrrd",
663
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0001.nrrd",
664
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0001.nrrd",
665
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0001.nrrd",
666
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0001.nrrd",
667
+ "label": 1.0,
668
+ "pirads": 4.0,
669
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0001.nrrd",
670
+ "psa": [
671
+ 5.8,
672
+ 61.0
673
+ ]
674
+ },
675
+ {
676
+ "image": "0048.nrrd",
677
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0048.nrrd",
678
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0048.nrrd",
679
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0048.nrrd",
680
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0048.nrrd",
681
+ "label": 1.0,
682
+ "pirads": 5.0,
683
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0048.nrrd",
684
+ "psa": [
685
+ 6.3,
686
+ 48.0
687
+ ]
688
+ },
689
+ {
690
+ "image": "0061.nrrd",
691
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0061.nrrd",
692
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0061.nrrd",
693
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0061.nrrd",
694
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0061.nrrd",
695
+ "label": 1.0,
696
+ "pirads": 5.0,
697
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0061.nrrd",
698
+ "psa": [
699
+ 20.0,
700
+ 51.0
701
+ ]
702
+ },
703
+ {
704
+ "image": "0002.nrrd",
705
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0002.nrrd",
706
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0002.nrrd",
707
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0002.nrrd",
708
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0002.nrrd",
709
+ "label": 1.0,
710
+ "pirads": 2.0,
711
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0002.nrrd",
712
+ "psa": [
713
+ 15.0,
714
+ 22.0
715
+ ]
716
+ },
717
+ {
718
+ "image": "0060.nrrd",
719
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0060.nrrd",
720
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0060.nrrd",
721
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0060.nrrd",
722
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0060.nrrd",
723
+ "label": 1.0,
724
+ "pirads": 4.0,
725
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0060.nrrd",
726
+ "psa": [
727
+ 5.8,
728
+ 47.0
729
+ ]
730
+ },
731
+ {
732
+ "image": "0046.nrrd",
733
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0046.nrrd",
734
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0046.nrrd",
735
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0046.nrrd",
736
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0046.nrrd",
737
+ "label": 0.0,
738
+ "pirads": 4.0,
739
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0046.nrrd",
740
+ "psa": [
741
+ 4.0,
742
+ 80.0
743
+ ]
744
+ },
745
+ {
746
+ "image": "0028.nrrd",
747
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0028.nrrd",
748
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0028.nrrd",
749
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0028.nrrd",
750
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0028.nrrd",
751
+ "label": 1.0,
752
+ "pirads": 4.0,
753
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0028.nrrd",
754
+ "psa": [
755
+ 28.0,
756
+ 41.0
757
+ ]
758
+ },
759
+ {
760
+ "image": "0022.nrrd",
761
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0022.nrrd",
762
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0022.nrrd",
763
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0022.nrrd",
764
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0022.nrrd",
765
+ "label": 1.0,
766
+ "pirads": 4.0,
767
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0022.nrrd",
768
+ "psa": [
769
+ 5.65,
770
+ 40.0
771
+ ]
772
+ },
773
+ {
774
+ "image": "0081.nrrd",
775
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0081.nrrd",
776
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0081.nrrd",
777
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0081.nrrd",
778
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0081.nrrd",
779
+ "label": 1.0,
780
+ "pirads": 5.0,
781
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0081.nrrd",
782
+ "psa": [
783
+ 5.0,
784
+ 27.0
785
+ ]
786
+ },
787
+ {
788
+ "image": "0004.nrrd",
789
+ "mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/prostate_mask/0004.nrrd",
790
+ "dwi": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/DWI_registered/0004.nrrd",
791
+ "adc": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/ADC_clipped/0004.nrrd",
792
+ "heatmap": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/heatmaps/0004.nrrd",
793
+ "label": 1.0,
794
+ "pirads": 4.0,
795
+ "smooth_mask": "/sc-projects/sc-proj-cc06-ag-ki-radiologie/prostate_test/COMFORT_data_mpMRI/processed/smooth_prostate_mask/0004.nrrd",
796
+ "psa": [
797
+ 6.03,
798
+ 49.0
799
+ ]
800
+ }
801
+ ]
802
+ }
job_scripts/{train_cspca_2.sh → test_cspca.sh} RENAMED
@@ -1,5 +1,5 @@
1
  #!/bin/bash
2
- #SBATCH --job-name=cspca_training_70 # Specify job name
3
  #SBATCH --partition=gpu # Specify partition name
4
  #SBATCH --mem=128G
5
  #SBATCH --gres=gpu:1
@@ -16,4 +16,4 @@ conda activate foundation
16
  RUNDIR="/sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate"
17
 
18
 
19
- srun python -u $RUNDIR/run_cspca.py --mode train --config $RUNDIR/config/config_cspca_train_2.yaml
 
1
  #!/bin/bash
2
+ #SBATCH --job-name=cspca_test_psa_64_59 # Specify job name
3
  #SBATCH --partition=gpu # Specify partition name
4
  #SBATCH --mem=128G
5
  #SBATCH --gres=gpu:1
 
16
  RUNDIR="/sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate"
17
 
18
 
19
+ srun python -u $RUNDIR/run_cspca.py --mode test --config $RUNDIR/config/config_cspca_test.yaml
job_scripts/train_cspca.sh CHANGED
@@ -1,5 +1,5 @@
1
  #!/bin/bash
2
- #SBATCH --job-name=cspca_test_epoch20 # Specify job name
3
  #SBATCH --partition=gpu # Specify partition name
4
  #SBATCH --mem=128G
5
  #SBATCH --gres=gpu:1
@@ -16,4 +16,4 @@ conda activate foundation
16
  RUNDIR="/sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate"
17
 
18
 
19
- srun python -u $RUNDIR/run_cspca.py --mode test --config $RUNDIR/config/config_cspca_test.yaml
 
1
  #!/bin/bash
2
+ #SBATCH --job-name=cspca_train_psa_64 # Specify job name
3
  #SBATCH --partition=gpu # Specify partition name
4
  #SBATCH --mem=128G
5
  #SBATCH --gres=gpu:1
 
16
  RUNDIR="/sc-scratch/sc-scratch-cc06-ag-ki-radiologie/prostate_foundation/WSAttention-Prostate"
17
 
18
 
19
+ srun python -u $RUNDIR/run_cspca.py --mode train --config $RUNDIR/config/config_cspca_train.yaml
run_cspca.py CHANGED
@@ -4,10 +4,12 @@ import os
4
  import shutil
5
  import sys
6
  from pathlib import Path
 
7
 
8
  import torch
9
  import yaml
10
  from monai.utils import set_determinism
 
11
 
12
  from src.data.data_loader import get_dataloader
13
  from src.model.cspca_model import CSPCAModel
@@ -19,6 +21,14 @@ from src.utils import get_metrics, save_cspca_checkpoint, setup_logging
19
  def main_worker(args):
20
  mil_model = MILModel3D(num_classes=args.num_classes, mil_mode=args.mil_mode)
21
  cache_dir_path = Path(os.path.join(args.logdir, "cache"))
 
 
 
 
 
 
 
 
22
 
23
  if args.mode == "train":
24
  checkpoint = torch.load(args.checkpoint_pirads, weights_only=False, map_location="cpu")
@@ -133,6 +143,7 @@ def parse_args():
133
  "--no_heatmap", dest="use_heatmap", action="store_false", help="disable heatmap"
134
  )
135
  parser.set_defaults(use_heatmap=True)
 
136
  parser.add_argument("--workers", default=2, type=int, help="number of workers for data loading")
137
  # parser.add_argument("--dry-run", action="store_true")
138
  parser.add_argument("--checkpoint_pirads", default=None, help="Load PI-RADS model")
 
4
  import shutil
5
  import sys
6
  from pathlib import Path
7
+ import json
8
 
9
  import torch
10
  import yaml
11
  from monai.utils import set_determinism
12
+ from sklearn.preprocessing import StandardScaler
13
 
14
  from src.data.data_loader import get_dataloader
15
  from src.model.cspca_model import CSPCAModel
 
21
  def main_worker(args):
22
  mil_model = MILModel3D(num_classes=args.num_classes, mil_mode=args.mil_mode)
23
  cache_dir_path = Path(os.path.join(args.logdir, "cache"))
24
+
25
+ scaler = StandardScaler()
26
+ with open(os.path.join(args.project_dir, "dataset", "PICAI_cspca_updated_with_psa.json")) as f:
27
+ dataset_json = json.load(f)
28
+ train_clinical = [i['psa'] for i in dataset_json['train']]
29
+ _ = scaler.fit_transform(train_clinical)
30
+ args.psa_mean = scaler.mean_.tolist()
31
+ args.psa_std = scaler.scale_.tolist()
32
 
33
  if args.mode == "train":
34
  checkpoint = torch.load(args.checkpoint_pirads, weights_only=False, map_location="cpu")
 
143
  "--no_heatmap", dest="use_heatmap", action="store_false", help="disable heatmap"
144
  )
145
  parser.set_defaults(use_heatmap=True)
146
+ parser.add_argument("--use_psa", default=True, type=bool)
147
  parser.add_argument("--workers", default=2, type=int, help="number of workers for data loading")
148
  # parser.add_argument("--dry-run", action="store_true")
149
  parser.add_argument("--checkpoint_pirads", default=None, help="Load PI-RADS model")
run_inference.py CHANGED
@@ -3,6 +3,7 @@ import json
3
  import logging
4
  import os
5
  from pathlib import Path
 
6
 
7
  import torch
8
  import yaml
@@ -58,6 +59,7 @@ def parse_args():
58
  parser.add_argument("--num_classes", default=4, type=int)
59
  parser.add_argument("--mil_mode", default="att_trans", type=str)
60
  parser.add_argument("--use_heatmap", default=True, type=bool)
 
61
  parser.add_argument("--tile_size", default=64, type=int)
62
  parser.add_argument("--tile_count", default=24, type=int)
63
  parser.add_argument("--depth", default=3, type=int)
 
3
  import logging
4
  import os
5
  from pathlib import Path
6
+ import json
7
 
8
  import torch
9
  import yaml
 
59
  parser.add_argument("--num_classes", default=4, type=int)
60
  parser.add_argument("--mil_mode", default="att_trans", type=str)
61
  parser.add_argument("--use_heatmap", default=True, type=bool)
62
+ parser.add_argument("--use_psa", default=True, type=bool)
63
  parser.add_argument("--tile_size", default=64, type=int)
64
  parser.add_argument("--tile_count", default=24, type=int)
65
  parser.add_argument("--depth", default=3, type=int)
run_pirads.py CHANGED
@@ -229,6 +229,7 @@ def parse_args():
229
  "--no_heatmap", dest="use_heatmap", action="store_false", help="disable heatmap"
230
  )
231
  parser.set_defaults(use_heatmap=True)
 
232
  parser.add_argument("--workers", default=2, type=int, help="number of workers for data loading")
233
 
234
  parser.add_argument("--checkpoint", default=None, help="load existing checkpoint")
 
229
  "--no_heatmap", dest="use_heatmap", action="store_false", help="disable heatmap"
230
  )
231
  parser.set_defaults(use_heatmap=True)
232
+ parser.add_argument("--use_psa", default=False, type=bool)
233
  parser.add_argument("--workers", default=2, type=int, help="number of workers for data loading")
234
 
235
  parser.add_argument("--checkpoint", default=None, help="load existing checkpoint")
src/data/custom_transforms.py CHANGED
@@ -47,6 +47,25 @@ class DilateAndSaveMaskd(MapTransform):
47
  ) # Add channel dimension back
48
 
49
  return d
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
50
 
51
 
52
  class ClipMaskIntensityPercentiles(Transform):
 
47
  ) # Add channel dimension back
48
 
49
  return d
50
+
51
+ class NormalizePSAd(MapTransform):
52
+ """
53
+ Custom transform to dilate binary mask and save a copy.
54
+ """
55
+
56
+ def __init__(self, keys, mean, std):
57
+ super().__init__(keys)
58
+ self.mean = torch.tensor(mean)
59
+ self.std = torch.tensor(std)
60
+
61
+ def __call__(self, data):
62
+ d = dict(data)
63
+
64
+ for key in self.keys:
65
+ d[key] = torch.tensor(d[key], dtype=torch.float32)
66
+ d[key] = (d[key] - self.mean) / self.std
67
+
68
+ return d
69
 
70
 
71
  class ClipMaskIntensityPercentiles(Transform):
src/data/data_loader.py CHANGED
@@ -24,7 +24,9 @@ from .custom_transforms import (
24
  ClipMaskIntensityPercentilesd,
25
  ElementwiseProductd,
26
  NormalizeIntensity_customd,
 
27
  )
 
28
 
29
 
30
  def list_data_collate(batch: list):
@@ -48,92 +50,131 @@ def list_data_collate(batch: list):
48
 
49
  def data_transform(args: argparse.Namespace) -> Transform:
50
  if args.use_heatmap:
51
- '''
52
- transform = Compose(
53
- [
54
- LoadImaged(
55
- keys=["image", "mask", "dwi", "adc", "heatmap","smooth_mask"],
56
- reader="ITKReader",
57
- ensure_channel_first=True,
58
- dtype=np.float32,
59
- ),
60
- ClipMaskIntensityPercentilesd(keys=["image"], lower=0, upper=99.5, mask_key="mask"),
61
- ConcatItemsd(
62
- keys=["image", "dwi", "adc"], name="image", dim=0
63
- ), # stacks to (3, H, W)
64
- NormalizeIntensity_customd(keys=["image"], channel_wise=True, mask_key="mask"),
65
- ElementwiseProductd(keys=["heatmap", "mask"], output_key="final_heatmap"),
66
- RandWeightedCropd(
67
- keys=["image", "final_heatmap", "mask"],
68
- w_key="final_heatmap",
69
- spatial_size=(args.tile_size, args.tile_size, args.depth),
70
- num_samples=args.tile_count,
71
- ),
72
- EnsureTyped(keys=["label"], dtype=torch.float32),
73
- Transposed(keys=["image"], indices=(0, 3, 1, 2)),
74
- DeleteItemsd(keys=[ "dwi", "adc", "heatmap"]),
75
- ToTensord(keys=["image", "label", "final_heatmap", "mask"]),
76
- ]
77
- )
78
- '''
79
- transform = Compose(
80
- [
81
- LoadImaged(
82
- keys=["image", "mask", "dwi", "adc", "heatmap","smooth_mask"],
83
- reader="ITKReader",
84
- ensure_channel_first=True,
85
- dtype=np.float32,
86
- ),
87
- ClipMaskIntensityPercentilesd(keys=["image"], lower=0, upper=99.5, mask_key="mask"),
88
- ClipMaskIntensityPercentilesd(keys=["dwi"], lower=0, upper=99.5, mask_key="mask"),
89
- NormalizeIntensity_customd(keys=["image"], mask_key="mask"),
90
- NormalizeIntensity_customd(keys=["dwi"], mask_key="mask"),
91
- ConcatItemsd(
92
- keys=["image", "dwi", "adc"], name="image", dim=0
93
- ), # stacks to (3, H, W)
94
- ElementwiseProductd(keys=["heatmap", "smooth_mask"], output_key="final_heatmap"),
95
- RandCropByPosNegLabeld(
96
- keys=["image", "final_heatmap", "smooth_mask"],
97
- label_key="smooth_mask",
98
- spatial_size=(args.tile_size, args.tile_size, args.depth),
99
- pos=1,
100
- neg=0,
101
- num_samples=args.tile_count,
102
- ),
103
- EnsureTyped(keys=["label"], dtype=torch.float32),
104
- Transposed(keys=["image"], indices=(0, 3, 1, 2)),
105
- DeleteItemsd(keys=[ "dwi", "adc", "heatmap", "mask"]),
106
- ToTensord(keys=["image", "label", "final_heatmap", "smooth_mask"]),
107
- ]
108
- )
 
 
 
 
 
109
  else:
110
- transform = Compose(
111
- [
112
- LoadImaged(
113
- keys=["image", "mask", "dwi", "adc"],
114
- reader="ITKReader",
115
- ensure_channel_first=True,
116
- dtype=np.float32,
117
- ),
118
- ClipMaskIntensityPercentilesd(keys=["image"], lower=0, upper=99.5, mask_key="mask"),
119
- ConcatItemsd(
120
- keys=["image", "dwi", "adc"], name="image", dim=0
121
- ), # stacks to (3, H, W)
122
- NormalizeIntensityd(keys=["image"], channel_wise=True),
123
- RandCropByPosNegLabeld(
124
- keys=["image"],
125
- label_key="mask",
126
- spatial_size=(args.tile_size, args.tile_size, args.depth),
127
- pos=1,
128
- neg=0,
129
- num_samples=args.tile_count,
130
- ),
131
- EnsureTyped(keys=["label"], dtype=torch.float32),
132
- Transposed(keys=["image"], indices=(0, 3, 1, 2)),
133
- DeleteItemsd(keys=["mask", "dwi", "adc"]),
134
- ToTensord(keys=["image", "label"]),
135
- ]
136
- )
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
137
  return transform
138
 
139
 
 
24
  ClipMaskIntensityPercentilesd,
25
  ElementwiseProductd,
26
  NormalizeIntensity_customd,
27
+ NormalizePSAd,
28
  )
29
+ from sklearn.preprocessing import StandardScaler
30
 
31
 
32
  def list_data_collate(batch: list):
 
50
 
51
  def data_transform(args: argparse.Namespace) -> Transform:
52
  if args.use_heatmap:
53
+ if args.use_psa:
54
+ transform = Compose(
55
+ [
56
+ LoadImaged(
57
+ keys=["image", "mask", "dwi", "adc", "heatmap","smooth_mask"],
58
+ reader="ITKReader",
59
+ ensure_channel_first=True,
60
+ dtype=np.float32,
61
+ ),
62
+ ClipMaskIntensityPercentilesd(keys=["image"], lower=0, upper=99.5, mask_key="mask"),
63
+ ClipMaskIntensityPercentilesd(keys=["dwi"], lower=0, upper=99.5, mask_key="mask"),
64
+ NormalizeIntensity_customd(keys=["image"], mask_key="mask"),
65
+ NormalizeIntensity_customd(keys=["dwi"], mask_key="mask"),
66
+ ConcatItemsd(
67
+ keys=["image", "dwi", "adc"], name="image", dim=0
68
+ ), # stacks to (3, H, W)
69
+ ElementwiseProductd(keys=["heatmap", "smooth_mask"], output_key="final_heatmap"),
70
+ RandCropByPosNegLabeld(
71
+ keys=["image", "final_heatmap", "smooth_mask"],
72
+ label_key="smooth_mask",
73
+ spatial_size=(args.tile_size, args.tile_size, args.depth),
74
+ pos=1,
75
+ neg=0,
76
+ num_samples=args.tile_count,
77
+ ),
78
+ NormalizePSAd(keys=["psa"], mean=args.psa_mean, std=args.psa_std),
79
+ EnsureTyped(keys=["label", "psa"], dtype=torch.float32),
80
+ Transposed(keys=["image"], indices=(0, 3, 1, 2)),
81
+ DeleteItemsd(keys=[ "dwi", "adc", "heatmap", "mask"]),
82
+ ToTensord(keys=["image", "label", "final_heatmap", "smooth_mask", "psa"]),
83
+ ]
84
+ )
85
+ else:
86
+ transform = Compose(
87
+ [
88
+ LoadImaged(
89
+ keys=["image", "mask", "dwi", "adc", "heatmap","smooth_mask"],
90
+ reader="ITKReader",
91
+ ensure_channel_first=True,
92
+ dtype=np.float32,
93
+ ),
94
+ ClipMaskIntensityPercentilesd(keys=["image"], lower=0, upper=99.5, mask_key="mask"),
95
+ ClipMaskIntensityPercentilesd(keys=["dwi"], lower=0, upper=99.5, mask_key="mask"),
96
+ NormalizeIntensity_customd(keys=["image"], mask_key="mask"),
97
+ NormalizeIntensity_customd(keys=["dwi"], mask_key="mask"),
98
+ ConcatItemsd(
99
+ keys=["image", "dwi", "adc"], name="image", dim=0
100
+ ), # stacks to (3, H, W)
101
+ ElementwiseProductd(keys=["heatmap", "smooth_mask"], output_key="final_heatmap"),
102
+ RandCropByPosNegLabeld(
103
+ keys=["image", "final_heatmap", "smooth_mask"],
104
+ label_key="smooth_mask",
105
+ spatial_size=(args.tile_size, args.tile_size, args.depth),
106
+ pos=1,
107
+ neg=0,
108
+ num_samples=args.tile_count,
109
+ ),
110
+ EnsureTyped(keys=["label"], dtype=torch.float32),
111
+ Transposed(keys=["image"], indices=(0, 3, 1, 2)),
112
+ DeleteItemsd(keys=[ "dwi", "adc", "heatmap", "mask"]),
113
+ ToTensord(keys=["image", "label", "final_heatmap", "smooth_mask"]),
114
+ ]
115
+ )
116
  else:
117
+ if args.use_psa:
118
+ transform = Compose(
119
+ [
120
+ LoadImaged(
121
+ keys=["image", "mask", "dwi", "adc","smooth_mask"],
122
+ reader="ITKReader",
123
+ ensure_channel_first=True,
124
+ dtype=np.float32,
125
+ ),
126
+ ClipMaskIntensityPercentilesd(keys=["image"], lower=0, upper=99.5, mask_key="mask"),
127
+ ClipMaskIntensityPercentilesd(keys=["dwi"], lower=0, upper=99.5, mask_key="mask"),
128
+ NormalizeIntensity_customd(keys=["image"], mask_key="mask"),
129
+ NormalizeIntensity_customd(keys=["dwi"], mask_key="mask"),
130
+ ConcatItemsd(
131
+ keys=["image", "dwi", "adc"], name="image", dim=0
132
+ ), # stacks to (3, H, W)
133
+ RandCropByPosNegLabeld(
134
+ keys=["image", "smooth_mask"],
135
+ label_key="smooth_mask",
136
+ spatial_size=(args.tile_size, args.tile_size, args.depth),
137
+ pos=1,
138
+ neg=0,
139
+ num_samples=args.tile_count,
140
+ ),
141
+ NormalizePSAd(keys=["psa"], mean=args.psa_mean, std=args.psa_std),
142
+ EnsureTyped(keys=["label", "psa"], dtype=torch.float32),
143
+ Transposed(keys=["image"], indices=(0, 3, 1, 2)),
144
+ DeleteItemsd(keys=[ "dwi", "adc", "mask"]),
145
+ ToTensord(keys=["image", "label", "smooth_mask", "psa"]),
146
+ ]
147
+ )
148
+ else:
149
+ transform = Compose(
150
+ [
151
+ LoadImaged(
152
+ keys=["image", "mask", "dwi", "adc","smooth_mask"],
153
+ reader="ITKReader",
154
+ ensure_channel_first=True,
155
+ dtype=np.float32,
156
+ ),
157
+ ClipMaskIntensityPercentilesd(keys=["image"], lower=0, upper=99.5, mask_key="mask"),
158
+ ClipMaskIntensityPercentilesd(keys=["dwi"], lower=0, upper=99.5, mask_key="mask"),
159
+ NormalizeIntensity_customd(keys=["image"], mask_key="mask"),
160
+ NormalizeIntensity_customd(keys=["dwi"], mask_key="mask"),
161
+ ConcatItemsd(
162
+ keys=["image", "dwi", "adc"], name="image", dim=0
163
+ ), # stacks to (3, H, W)
164
+ RandCropByPosNegLabeld(
165
+ keys=["image", "smooth_mask"],
166
+ label_key="smooth_mask",
167
+ spatial_size=(args.tile_size, args.tile_size, args.depth),
168
+ pos=1,
169
+ neg=0,
170
+ num_samples=args.tile_count,
171
+ ),
172
+ EnsureTyped(keys=["label"], dtype=torch.float32),
173
+ Transposed(keys=["image"], indices=(0, 3, 1, 2)),
174
+ DeleteItemsd(keys=[ "dwi", "adc", "mask"]),
175
+ ToTensord(keys=["image", "label", "smooth_mask"]),
176
+ ]
177
+ )
178
  return transform
179
 
180
 
src/model/cspca_model.py CHANGED
@@ -71,10 +71,19 @@ class CSPCAModel(nn.Module):
71
  def __init__(self, backbone: nn.Module) -> None:
72
  super().__init__()
73
  self.backbone = backbone
 
 
 
 
 
 
 
 
 
74
  self.fc_dim = backbone.myfc.in_features
75
- self.fc_cspca = SimpleNN(input_dim=self.fc_dim)
76
 
77
- def forward(self, x):
78
  sh = x.shape
79
  x = x.reshape(sh[0] * sh[1], sh[2], sh[3], sh[4], sh[5])
80
  x = self.backbone.net(x)
@@ -85,6 +94,9 @@ class CSPCAModel(nn.Module):
85
  a = self.backbone.attention(x)
86
  a = torch.softmax(a, dim=1)
87
  x = torch.sum(x * a, dim=1)
 
 
 
88
 
89
  x = self.fc_cspca(x)
90
  return x
 
71
  def __init__(self, backbone: nn.Module) -> None:
72
  super().__init__()
73
  self.backbone = backbone
74
+
75
+ self.clinical_dim = 2
76
+ self.projection_dim = 32
77
+ self.clinical_projection = nn.Sequential(
78
+ nn.Linear(self.clinical_dim, self.projection_dim),
79
+ nn.ReLU(),
80
+ nn.BatchNorm1d(self.projection_dim) # Helps stabilize the merged scale
81
+ )
82
+
83
  self.fc_dim = backbone.myfc.in_features
84
+ self.fc_cspca = SimpleNN(input_dim=self.fc_dim + self.projection_dim)
85
 
86
+ def forward(self, x, psa_data):
87
  sh = x.shape
88
  x = x.reshape(sh[0] * sh[1], sh[2], sh[3], sh[4], sh[5])
89
  x = self.backbone.net(x)
 
94
  a = self.backbone.attention(x)
95
  a = torch.softmax(a, dim=1)
96
  x = torch.sum(x * a, dim=1)
97
+
98
+ psa_features = self.clinical_projection(psa_data)
99
+ x = torch.cat((x, psa_features), dim=1)
100
 
101
  x = self.fc_cspca(x)
102
  return x
src/train/train_cspca.py CHANGED
@@ -15,9 +15,10 @@ def train_epoch(cspca_model, loader, optimizer, epoch, args):
15
  for _, batch_data in enumerate(loader):
16
  data = batch_data["image"].as_subclass(torch.Tensor).to(args.device)
17
  target = batch_data["label"].as_subclass(torch.Tensor).to(args.device)
 
18
 
19
  optimizer.zero_grad()
20
- output = cspca_model(data)
21
  output = output.squeeze(1)
22
  loss = criterion(output, target)
23
  loss.backward()
@@ -46,8 +47,9 @@ def val_epoch(cspca_model, loader, epoch, args):
46
  for _, batch_data in enumerate(loader):
47
  data = batch_data["image"].as_subclass(torch.Tensor).to(args.device)
48
  target = batch_data["label"].as_subclass(torch.Tensor).to(args.device)
 
49
 
50
- output = cspca_model(data)
51
  output = output.squeeze(1)
52
  loss = criterion(output, target)
53
 
 
15
  for _, batch_data in enumerate(loader):
16
  data = batch_data["image"].as_subclass(torch.Tensor).to(args.device)
17
  target = batch_data["label"].as_subclass(torch.Tensor).to(args.device)
18
+ psa_data = batch_data["psa"].as_subclass(torch.Tensor).to(args.device)
19
 
20
  optimizer.zero_grad()
21
+ output = cspca_model(x = data, psa_data = psa_data)
22
  output = output.squeeze(1)
23
  loss = criterion(output, target)
24
  loss.backward()
 
47
  for _, batch_data in enumerate(loader):
48
  data = batch_data["image"].as_subclass(torch.Tensor).to(args.device)
49
  target = batch_data["label"].as_subclass(torch.Tensor).to(args.device)
50
+ psa_data = batch_data["psa"].as_subclass(torch.Tensor).to(args.device)
51
 
52
+ output = cspca_model(x = data, psa_data = psa_data)
53
  output = output.squeeze(1)
54
  loss = criterion(output, target)
55
 
temp_2.ipynb CHANGED
The diff for this file is too large to render. See raw diff