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  1. environment.txt +113 -0
  2. groups/TEST/data.tsv +3 -0
  3. groups/TEST/maps.json +4 -0
  4. groups/TEST2/data.tsv +9 -0
  5. groups/TEST2/maps.json +4 -0
  6. groups/TEST3/data.tsv +9 -0
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  8. groups/TEST4/data.tsv +9 -0
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  50. split-0/best-loss/validation/validation_image_level_prediction.tsv +94 -0
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2000
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groups/train/split-0/data.tsv ADDED
@@ -0,0 +1,372 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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253
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254
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259
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260
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268
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331
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332
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367
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368
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369
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370
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371
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372
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groups/train/split-0/maps.json ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ {
2
+ "caps_directory": "/gpfswork/rech/krk/upd53tc/../commun/datasets/adni/caps/caps_v2021/",
3
+ "multi_cohort": false
4
+ }
groups/train/split-1/data.tsv ADDED
@@ -0,0 +1,372 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ participant_id session_id cohort diagnosis
2
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groups/train/split-1/maps.json ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ {
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+ "caps_directory": "/gpfswork/rech/krk/upd53tc/../commun/datasets/adni/caps/caps_v2021/",
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+ "multi_cohort": false
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+ }
groups/train/split-2/data.tsv ADDED
@@ -0,0 +1,372 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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groups/train/split-2/maps.json ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ {
2
+ "caps_directory": "/gpfswork/rech/krk/upd53tc/../commun/datasets/adni/caps/caps_v2021/",
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+ "multi_cohort": false
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+ }
groups/train/split-3/data.tsv ADDED
@@ -0,0 +1,373 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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groups/train/split-3/maps.json ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ {
2
+ "caps_directory": "/gpfswork/rech/krk/upd53tc/../commun/datasets/adni/caps/caps_v2021/",
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+ "multi_cohort": false
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+ }
groups/train/split-4/data.tsv ADDED
@@ -0,0 +1,372 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ participant_id session_id cohort diagnosis
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243
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244
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groups/train/split-4/maps.json ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ {
2
+ "caps_directory": "/gpfswork/rech/krk/upd53tc/../commun/datasets/adni/caps/caps_v2021/",
3
+ "multi_cohort": false
4
+ }
groups/validation/split-0/data.tsv ADDED
@@ -0,0 +1,94 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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groups/validation/split-0/maps.json ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ {
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3
+ "multi_cohort": false
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groups/validation/split-1/data.tsv ADDED
@@ -0,0 +1,94 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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groups/validation/split-1/maps.json ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ {
2
+ "caps_directory": "/gpfswork/rech/krk/upd53tc/../commun/datasets/adni/caps/caps_v2021/",
3
+ "multi_cohort": false
4
+ }
groups/validation/split-2/data.tsv ADDED
@@ -0,0 +1,94 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ participant_id session_id cohort diagnosis
2
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3
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4
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5
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17
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18
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19
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20
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22
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23
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24
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25
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26
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27
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29
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30
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31
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32
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33
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34
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35
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36
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37
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42
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43
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44
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45
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46
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47
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48
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50
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51
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52
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53
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54
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55
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57
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60
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62
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65
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68
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70
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71
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72
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88
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92
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93
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94
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groups/validation/split-2/maps.json ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ {
2
+ "caps_directory": "/gpfswork/rech/krk/upd53tc/../commun/datasets/adni/caps/caps_v2021/",
3
+ "multi_cohort": false
4
+ }
groups/validation/split-3/data.tsv ADDED
@@ -0,0 +1,93 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ participant_id session_id cohort diagnosis
2
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32
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33
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34
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35
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36
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37
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38
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39
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40
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41
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42
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43
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44
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45
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46
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51
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52
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53
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54
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55
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56
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57
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58
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60
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61
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62
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63
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68
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72
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76
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78
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80
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81
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88
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91
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92
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93
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groups/validation/split-3/maps.json ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ {
2
+ "caps_directory": "/gpfswork/rech/krk/upd53tc/../commun/datasets/adni/caps/caps_v2021/",
3
+ "multi_cohort": false
4
+ }
groups/validation/split-4/data.tsv ADDED
@@ -0,0 +1,94 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ participant_id session_id cohort diagnosis
2
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3
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4
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5
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6
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7
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8
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10
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11
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14
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15
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16
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17
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18
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19
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20
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22
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23
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25
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26
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27
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28
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29
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30
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31
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32
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33
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34
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35
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36
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37
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38
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39
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40
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41
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42
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43
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44
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45
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46
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47
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48
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49
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50
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51
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52
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53
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54
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55
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56
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60
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61
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62
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63
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68
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69
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70
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71
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93
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94
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groups/validation/split-4/maps.json ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ {
2
+ "caps_directory": "/gpfswork/rech/krk/upd53tc/../commun/datasets/adni/caps/caps_v2021/",
3
+ "multi_cohort": false
4
+ }
maps.json ADDED
@@ -0,0 +1,72 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architecture": "Conv4_FC3",
3
+ "multi_network": false,
4
+ "dropout": 0.0,
5
+ "latent_space_dimension": 64,
6
+ "latent_space_size": 2,
7
+ "selection_metrics": [
8
+ "loss"
9
+ ],
10
+ "label": "diagnosis",
11
+ "selection_threshold": 0.0,
12
+ "gpu": true,
13
+ "n_proc": 32,
14
+ "batch_size": 32,
15
+ "evaluation_steps": 20,
16
+ "seed": 0,
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+ "deterministic": false,
18
+ "compensation": "memory",
19
+ "transfer_path": "../../autoencoders/exp3/maps",
20
+ "transfer_selection_metric": "loss",
21
+ "use_extracted_features": false,
22
+ "multi_cohort": false,
23
+ "diagnoses": [
24
+ "AD",
25
+ "CN"
26
+ ],
27
+ "baseline": true,
28
+ "normalize": true,
29
+ "data_augmentation": false,
30
+ "sampler": "random",
31
+ "n_splits": 5,
32
+ "epochs": 200,
33
+ "learning_rate": 1e-05,
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+ "weight_decay": 0.0001,
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+ "patience": 10,
36
+ "tolerance": 0.0,
37
+ "accumulation_steps": 1,
38
+ "optimizer": "Adam",
39
+ "preprocessing_dict": {
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+ "preprocessing": "t1-linear",
41
+ "mode": "roi",
42
+ "use_uncropped_image": false,
43
+ "roi_list": [
44
+ "leftHippocampusBox",
45
+ "rightHippocampusBox"
46
+ ],
47
+ "uncropped_roi": false,
48
+ "prepare_dl": false,
49
+ "file_type": {
50
+ "pattern": "*space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_T1w.nii.gz",
51
+ "description": "T1W Image registered using t1-linear and cropped (matrix size 169\u00d7208\u00d7179, 1 mm isotropic voxels)",
52
+ "needed_pipeline": "t1-linear"
53
+ }
54
+ },
55
+ "mode": "roi",
56
+ "network_task": "classification",
57
+ "caps_directory": "$WORK/../commun/datasets/adni/caps/caps_v2021/",
58
+ "tsv_path": "$WORK/Aramis_tools/ClinicaDL_tools/experiments_ADDL/data/ADNI/train",
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+ "validation": "KFoldSplit",
60
+ "num_networks": 2,
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+ "label_code": {
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+ "AD": 0,
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+ "CN": 1
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+ },
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+ "output_size": 2,
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+ "input_size": [
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+ 1,
68
+ 50,
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+ 50,
70
+ 50
71
+ ]
72
+ }
split-0/best-loss/TEST2/TEST2_image_level_metrics.tsv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ accuracy sensitivity specificity PPV NPV BA
2
+ 0.25 0.25 0.25 0.25 0.25 0.25
split-0/best-loss/TEST2/TEST2_image_level_prediction.tsv ADDED
@@ -0,0 +1,9 @@
 
 
 
 
 
 
 
 
 
 
1
+ participant_id session_id roi_id true_label predicted_label proba0 proba1
2
+ sub-OAS30010 ses-M000 0 0 1 0.24481599753902805 0.7551840005382415
3
+ sub-OAS30011 ses-M000 0 0 1 0.4385076982359733 0.5614923027253921
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+ sub-OAS30011 ses-M054 0 1 0 0.9807814455801442 0.019218513201321265
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+ sub-OAS30012 ses-M006 0 1 0 0.9290627510316911 0.07093730175326905
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+ sub-OAS30012 ses-M018 0 1 0 0.9812280170379148 0.018772025562582416
7
+ sub-OAS30013 ses-M006 0 0 0 0.9371386631842584 0.06286133128789156
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+ sub-OAS30014 ses-M006 0 1 1 0.043138640061501504 0.9568613671487378
9
+ sub-OAS30014 ses-M036 0 0 1 0.013301646757510367 0.9866983755942316
split-0/best-loss/TEST2/TEST2_roi_level_metrics.tsv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ accuracy sensitivity specificity PPV NPV BA loss
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split-0/best-loss/train/train_roi_level_prediction.tsv ADDED
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split-0/best-loss/validation/description.log ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ Prediction validation group - 2022-02-02 12:34:10.932173
2
+ Data loaded from CAPS directories: {'single': '/gpfswork/rech/krk/upd53tc/../commun/datasets/adni/caps/caps_v2021/'}
3
+ Number of participants: 93
4
+ Number of sessions: 93
split-0/best-loss/validation/validation_image_level_metrics.tsv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ accuracy sensitivity specificity PPV NPV BA
2
+ 0.8709677419354839 0.8333333333333334 0.9111111111111111 0.9090909090909091 0.8367346938775511 0.8722222222222222
split-0/best-loss/validation/validation_image_level_prediction.tsv ADDED
@@ -0,0 +1,94 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ participant_id session_id roi_id true_label predicted_label proba0 proba1
2
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