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AQC_dataset

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  1. .claude/settings.local.json +47 -0
  2. acdc_qc_dataset.json +152 -0
  3. create_acdc_json.py +45 -0
  4. raw_dataset/ACDC_original/.gitattributes +54 -0
  5. raw_dataset/ACDC_original/README.md +28 -0
  6. raw_dataset/ACDC_original/testing/MANDATORY_CITATION.md +5 -0
  7. raw_dataset/ACDC_original/testing/patient101/Info.cfg +6 -0
  8. raw_dataset/ACDC_original/testing/patient101/MANDATORY_CITATION.md +5 -0
  9. raw_dataset/ACDC_original/testing/patient101/patient101_4d.nii.gz +3 -0
  10. raw_dataset/ACDC_original/testing/patient101/patient101_frame01.nii.gz +3 -0
  11. raw_dataset/ACDC_original/testing/patient101/patient101_frame01_gt.nii.gz +3 -0
  12. raw_dataset/ACDC_original/testing/patient101/patient101_frame14.nii.gz +3 -0
  13. raw_dataset/ACDC_original/testing/patient101/patient101_frame14_gt.nii.gz +3 -0
  14. raw_dataset/ACDC_original/testing/patient102/Info.cfg +6 -0
  15. raw_dataset/ACDC_original/testing/patient102/MANDATORY_CITATION.md +5 -0
  16. raw_dataset/ACDC_original/testing/patient102/patient102_4d.nii.gz +3 -0
  17. raw_dataset/ACDC_original/testing/patient102/patient102_frame01.nii.gz +3 -0
  18. raw_dataset/ACDC_original/testing/patient102/patient102_frame01_gt.nii.gz +3 -0
  19. raw_dataset/ACDC_original/testing/patient102/patient102_frame13.nii.gz +3 -0
  20. raw_dataset/ACDC_original/testing/patient102/patient102_frame13_gt.nii.gz +3 -0
  21. raw_dataset/ACDC_original/testing/patient103/Info.cfg +6 -0
  22. raw_dataset/ACDC_original/testing/patient103/MANDATORY_CITATION.md +5 -0
  23. raw_dataset/ACDC_original/testing/patient103/patient103_4d.nii.gz +3 -0
  24. raw_dataset/ACDC_original/testing/patient103/patient103_frame01.nii.gz +3 -0
  25. raw_dataset/ACDC_original/testing/patient103/patient103_frame01_gt.nii.gz +3 -0
  26. raw_dataset/ACDC_original/testing/patient103/patient103_frame11.nii.gz +3 -0
  27. raw_dataset/ACDC_original/testing/patient103/patient103_frame11_gt.nii.gz +3 -0
  28. raw_dataset/ACDC_original/testing/patient104/Info.cfg +6 -0
  29. raw_dataset/ACDC_original/testing/patient104/MANDATORY_CITATION.md +5 -0
  30. raw_dataset/ACDC_original/testing/patient104/patient104_4d.nii.gz +3 -0
  31. raw_dataset/ACDC_original/testing/patient104/patient104_frame01.nii.gz +3 -0
  32. raw_dataset/ACDC_original/testing/patient104/patient104_frame01_gt.nii.gz +3 -0
  33. raw_dataset/ACDC_original/testing/patient104/patient104_frame11.nii.gz +3 -0
  34. raw_dataset/ACDC_original/testing/patient104/patient104_frame11_gt.nii.gz +3 -0
  35. raw_dataset/ACDC_original/testing/patient105/Info.cfg +6 -0
  36. raw_dataset/ACDC_original/testing/patient105/MANDATORY_CITATION.md +5 -0
  37. raw_dataset/ACDC_original/testing/patient105/patient105_4d.nii.gz +3 -0
  38. raw_dataset/ACDC_original/testing/patient105/patient105_frame01.nii.gz +3 -0
  39. raw_dataset/ACDC_original/testing/patient105/patient105_frame01_gt.nii.gz +3 -0
  40. raw_dataset/ACDC_original/testing/patient105/patient105_frame10.nii.gz +3 -0
  41. raw_dataset/ACDC_original/testing/patient105/patient105_frame10_gt.nii.gz +3 -0
  42. raw_dataset/ACDC_original/testing/patient106/Info.cfg +6 -0
  43. raw_dataset/ACDC_original/testing/patient106/MANDATORY_CITATION.md +5 -0
  44. raw_dataset/ACDC_original/testing/patient106/patient106_4d.nii.gz +3 -0
  45. raw_dataset/ACDC_original/testing/patient106/patient106_frame01.nii.gz +3 -0
  46. raw_dataset/ACDC_original/testing/patient106/patient106_frame01_gt.nii.gz +3 -0
  47. raw_dataset/ACDC_original/testing/patient106/patient106_frame13.nii.gz +3 -0
  48. raw_dataset/ACDC_original/testing/patient106/patient106_frame13_gt.nii.gz +3 -0
  49. raw_dataset/ACDC_original/testing/patient107/Info.cfg +6 -0
  50. raw_dataset/ACDC_original/testing/patient107/MANDATORY_CITATION.md +5 -0
.claude/settings.local.json ADDED
@@ -0,0 +1,47 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "permissions": {
3
+ "allow": [
4
+ "Read(//mnt/storage/home/ym1413/cardiac/HCMNIH/public_dataset/ACDC/**)",
5
+ "Read(//mnt/storage/home/ym1413/cardiac/HCMNIH/public_dataset/**)",
6
+ "Bash(wget --version)",
7
+ "Bash(curl --version)",
8
+ "Read(//usr/bin/**)",
9
+ "Bash(huggingface-cli download qicq1c/ACDC --repo-type dataset --local-dir ./ACDC)",
10
+ "Bash(huggingface-cli --version)",
11
+ "Bash(pip install huggingface-hub)",
12
+ "Bash(/usr/bin/python2.7 -c \"print(''Python works'')\")",
13
+ "WebSearch",
14
+ "Bash(chmod +x /mnt/storage/home/ym1413/QC_data_preprocessing/rename_acdc_data.py)",
15
+ "Bash(for dir in patient001 patient002 patient003)",
16
+ "Bash(do echo \"=== $dir ===\")",
17
+ "Bash(ls $dir/*frame*.nii.gz)",
18
+ "Bash(done)",
19
+ "Bash(python /mnt/storage/home/ym1413/QC_data_preprocessing/rename_acdc_specific.py --dry-run)",
20
+ "Read(//mnt/storage/home/ym1413/nnunet_src/**)",
21
+ "Bash(python /mnt/storage/home/ym1413/QC_data_preprocessing/create_acdc_json.py)",
22
+ "Bash(git:*)",
23
+ "Bash(conda install:*)",
24
+ "Bash(python3:*)",
25
+ "Bash(unzip -q Images.zip)",
26
+ "Bash(unzip -q Masks.zip)",
27
+ "Bash(curl -s \"https://huggingface.co/api/datasets?search=ACDC+cardiac&limit=20\")",
28
+ "Bash(curl -s \"https://huggingface.co/api/datasets?search=ACDC&limit=30\")",
29
+ "Bash(curl -s \"https://huggingface.co/api/datasets/msepulvedagodoy/acdc/tree/main\")",
30
+ "Bash(curl -s \"https://huggingface.co/api/datasets/Angelou0516/ACDC/tree/main\")",
31
+ "Bash(curl -s \"https://huggingface.co/api/datasets/czotti/acdc/tree/main\")",
32
+ "Bash(curl -s \"https://huggingface.co/api/datasets/nevereverinsomnia/ACDC_MICCAI_2017/tree/main\")",
33
+ "Bash(curl -s \"https://huggingface.co/api/datasets/viennh2012/cardiac_cine_acdc/tree/main\")",
34
+ "Bash(curl -s \"https://huggingface.co/api/datasets/zhuyinheng/acdc/tree/main\")",
35
+ "Bash(curl -s \"https://huggingface.co/api/datasets/msepulvedagodoy/acdc/tree/main/training\")",
36
+ "Bash(curl -s \"https://huggingface.co/api/datasets/Angelou0516/ACDC/tree/main/training\")",
37
+ "Bash(curl -s \"https://huggingface.co/api/datasets/zhuyinheng/acdc/tree/main/training\")",
38
+ "Bash(curl -s \"https://huggingface.co/api/datasets/msepulvedagodoy/acdc/tree/main/training/patient001\")",
39
+ "Bash(curl -s \"https://huggingface.co/api/datasets/msepulvedagodoy/acdc/tree/main/testing\")",
40
+ "Bash(curl -s \"https://huggingface.co/api/datasets/Angelou0516/ACDC/tree/main/training/patient001\")",
41
+ "Bash(curl -s \"https://huggingface.co/api/datasets/msepulvedagodoy/acdc/tree/main/testing/patient101\")",
42
+ "Bash(curl:*)"
43
+ ],
44
+ "deny": [],
45
+ "ask": []
46
+ }
47
+ }
acdc_qc_dataset.json ADDED
@@ -0,0 +1,152 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient001": {},
3
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient002": {},
4
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient003": {},
5
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient004": {},
6
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient005": {},
7
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient006": {},
8
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient007": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient008": {},
10
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient009": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient010": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient011": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient012": {},
14
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient013": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient014": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient015": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient016": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient017": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient018": {},
20
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient019": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient020": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient021": {},
23
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient022": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient023": {},
25
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient024": {},
26
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient025": {},
27
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient026": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient027": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient028": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient029": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient030": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient031": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient032": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient033": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient034": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient035": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient036": {},
38
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient037": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient038": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient039": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient040": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient041": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient042": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient043": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient044": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient045": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient046": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient047": {},
49
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient048": {},
50
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient049": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient050": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient051": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient052": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient053": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient054": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient055": {},
57
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient056": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient057": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient058": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient059": {},
61
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient060": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient061": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient062": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient063": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient064": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient065": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient066": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient067": {},
69
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient068": {},
70
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient069": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient070": {},
72
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient071": {},
73
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient072": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient073": {},
75
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient074": {},
76
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient075": {},
77
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient076": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient077": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient078": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient079": {},
81
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient080": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient081": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient082": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient083": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient084": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient085": {},
87
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient086": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient087": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient088": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient089": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient090": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient091": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient092": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient093": {},
95
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient094": {},
96
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient095": {},
97
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient096": {},
98
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient097": {},
99
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient098": {},
100
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient099": {},
101
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient100": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient101": {},
103
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient102": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient103": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient104": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient105": {},
107
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient106": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient107": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient108": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient109": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient110": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient111": {},
113
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient112": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient113": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient114": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient115": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient116": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient117": {},
119
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient118": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient119": {},
121
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient120": {},
122
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient121": {},
123
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient122": {},
124
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient123": {},
125
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient124": {},
126
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient125": {},
127
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient126": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient127": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient128": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient129": {},
131
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient130": {},
132
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient131": {},
133
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient132": {},
134
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient133": {},
135
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient134": {},
136
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient135": {},
137
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient136": {},
138
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient137": {},
139
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient138": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient139": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient140": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient141": {},
143
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient142": {},
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+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient143": {},
145
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient144": {},
146
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient145": {},
147
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient146": {},
148
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient147": {},
149
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient148": {},
150
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient149": {},
151
+ "/cardiac/HCMNIH/public_dataset/ACDC/QC/ori/patient150": {}
152
+ }
create_acdc_json.py ADDED
@@ -0,0 +1,45 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ """
3
+ Create JSON file for ACDC QC software with patient folder paths as keys
4
+ """
5
+
6
+ import json
7
+ from pathlib import Path
8
+
9
+ def create_acdc_json():
10
+ # Base directory for ACDC data (output of rename_acdc_specific.py)
11
+ base_dir = Path("/mnt/storage/home/ym1413/QC_data_preprocessing/sabotaged_dataset")
12
+
13
+ # Create dictionary with patient folders as keys
14
+ acdc_data = {}
15
+
16
+ # Get all patient directories
17
+ patient_dirs = sorted([d for d in base_dir.iterdir() if d.is_dir() and d.name.startswith('patient')])
18
+
19
+ for patient_dir in patient_dirs:
20
+ # Remove base path /mnt/storage/home/ym1413 from the key
21
+ key = str(patient_dir).replace("/mnt/storage/home/ym1413", "")
22
+
23
+ # Extract patient ID from folder name
24
+ patient_id = patient_dir.name
25
+
26
+ # Create entry for this patient - just the key with empty dict for QC software to populate
27
+ acdc_data[key] = {}
28
+
29
+ # Save to JSON file
30
+ output_file = Path("/mnt/storage/home/ym1413/QC_data_preprocessing/acdc_qc_dataset.json")
31
+
32
+ with open(output_file, 'w') as f:
33
+ json.dump(acdc_data, f, indent=4, sort_keys=True)
34
+
35
+ print(f"Created JSON file with {len(acdc_data)} patient entries")
36
+ print(f"Output saved to: {output_file}")
37
+
38
+ # Show first few entries as preview
39
+ print("\nFirst 3 entries:")
40
+ for i, key in enumerate(list(acdc_data.keys())[:3]):
41
+ print(f"\nEntry {i+1}:")
42
+ print(f" Key: {key}")
43
+
44
+ if __name__ == "__main__":
45
+ create_acdc_json()
raw_dataset/ACDC_original/.gitattributes ADDED
@@ -0,0 +1,54 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ *.7z filter=lfs diff=lfs merge=lfs -text
2
+ *.arrow filter=lfs diff=lfs merge=lfs -text
3
+ *.bin filter=lfs diff=lfs merge=lfs -text
4
+ *.bz2 filter=lfs diff=lfs merge=lfs -text
5
+ *.ckpt filter=lfs diff=lfs merge=lfs -text
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+ *.ftz filter=lfs diff=lfs merge=lfs -text
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+ *.gz filter=lfs diff=lfs merge=lfs -text
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+ *.h5 filter=lfs diff=lfs merge=lfs -text
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+ *.joblib filter=lfs diff=lfs merge=lfs -text
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+ *.lfs.* filter=lfs diff=lfs merge=lfs -text
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+ *.lz4 filter=lfs diff=lfs merge=lfs -text
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+ *.mlmodel filter=lfs diff=lfs merge=lfs -text
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+ *.model filter=lfs diff=lfs merge=lfs -text
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+ *.msgpack filter=lfs diff=lfs merge=lfs -text
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+ *.npy filter=lfs diff=lfs merge=lfs -text
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+ *.npz filter=lfs diff=lfs merge=lfs -text
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+ *.onnx filter=lfs diff=lfs merge=lfs -text
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+ *.ot filter=lfs diff=lfs merge=lfs -text
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+ *.parquet filter=lfs diff=lfs merge=lfs -text
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+ *.pb filter=lfs diff=lfs merge=lfs -text
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+ *.pickle filter=lfs diff=lfs merge=lfs -text
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+ *.pkl filter=lfs diff=lfs merge=lfs -text
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+ *.pt filter=lfs diff=lfs merge=lfs -text
24
+ *.pth filter=lfs diff=lfs merge=lfs -text
25
+ *.rar filter=lfs diff=lfs merge=lfs -text
26
+ *.safetensors filter=lfs diff=lfs merge=lfs -text
27
+ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
28
+ *.tar.* filter=lfs diff=lfs merge=lfs -text
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+ *.tflite filter=lfs diff=lfs merge=lfs -text
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+ *.tgz filter=lfs diff=lfs merge=lfs -text
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+ *.wasm filter=lfs diff=lfs merge=lfs -text
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+ *.xz filter=lfs diff=lfs merge=lfs -text
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+ *.zip filter=lfs diff=lfs merge=lfs -text
34
+ *.zst filter=lfs diff=lfs merge=lfs -text
35
+ *tfevents* filter=lfs diff=lfs merge=lfs -text
36
+ # Audio files - uncompressed
37
+ *.pcm filter=lfs diff=lfs merge=lfs -text
38
+ *.sam filter=lfs diff=lfs merge=lfs -text
39
+ *.raw filter=lfs diff=lfs merge=lfs -text
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+ # Audio files - compressed
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+ *.aac filter=lfs diff=lfs merge=lfs -text
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+ *.flac filter=lfs diff=lfs merge=lfs -text
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+ *.mp3 filter=lfs diff=lfs merge=lfs -text
44
+ *.ogg filter=lfs diff=lfs merge=lfs -text
45
+ *.wav filter=lfs diff=lfs merge=lfs -text
46
+ # Image files - uncompressed
47
+ *.bmp filter=lfs diff=lfs merge=lfs -text
48
+ *.gif filter=lfs diff=lfs merge=lfs -text
49
+ *.png filter=lfs diff=lfs merge=lfs -text
50
+ *.tiff filter=lfs diff=lfs merge=lfs -text
51
+ # Image files - compressed
52
+ *.jpg filter=lfs diff=lfs merge=lfs -text
53
+ *.jpeg filter=lfs diff=lfs merge=lfs -text
54
+ *.webp filter=lfs diff=lfs merge=lfs -text
raw_dataset/ACDC_original/README.md ADDED
@@ -0,0 +1,28 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ---
2
+ task_categories:
3
+ - image-segmentation
4
+ language:
5
+ - es
6
+ - en
7
+ tags:
8
+ - medical
9
+ pretty_name: ACDC-Automated Cardiac Diagnosis Challenge
10
+ size_categories:
11
+ - 1K<n<10K
12
+ ---
13
+
14
+ ![Screenshot 2023-06-11 at 23.19.31.png](https://s3.amazonaws.com/moonup/production/uploads/6226bae1c8655fec3995a41d/cO9OKcYBO7-MbDZJopF6J.png)
15
+
16
+ General information
17
+
18
+ The overall ACDC dataset was created from real clinical exams acquired at the University Hospital of Dijon. Acquired data were fully anonymized and handled within the regulations set by the local ethical committee of the Hospital of Dijon (France). Our dataset covers several well-defined pathologies with enough cases to (1) properly train machine learning methods and (2) clearly assess the variations of the main physiological parameters obtained from cine-MRI (in particular diastolic volume and ejection fraction). The dataset is composed of 150 exams (all from different patients) divided into 5 evenly distributed subgroups (4 pathological plus 1 healthy subject groups) as described below. Furthermore, each patient comes with the following additional information : weight, height, as well as the diastolic and systolic phase instants.
19
+
20
+ Tasks
21
+
22
+ The main task of this dataset is the semantic segmentation of the heart in cardiac magnetic resonance images, specifically the endocardium and myocardium. The present task is very relevant for the detection of cardiovascular diseases. Segmentation is a very time-consuming process, so automatically performing the segmentation with Artificial Intelligence algorithms can be extremely beneficial to reduce the time spent in a manual segmentation. In this way, a very relevant bottleneck can be avoided and cardiovascular diseases can be detected in a timely manner.
23
+
24
+ Reference
25
+
26
+ O. Bernard, A. Lalande, C. Zotti, F. Cervenansky, et al.
27
+ "Deep Learning Techniques for Automatic MRI Cardiac Multi-structures Segmentation and Diagnosis: Is the Problem Solved ?" in IEEE Transactions on Medical Imaging, vol. 37, no. 11, pp. 2514-2525, Nov. 2018
28
+ doi: 10.1109/TMI.2018.2837502
raw_dataset/ACDC_original/testing/MANDATORY_CITATION.md ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ You have to refer to this citation for any use of the ACDC database
2
+
3
+ O. Bernard, A. Lalande, C. Zotti, F. Cervenansky, et al.
4
+ "Deep Learning Techniques for Automatic MRI Cardiac Multi-structures Segmentation and Diagnosis: Is the Problem Solved ?" in IEEE Transactions on Medical Imaging, vol. 37, no. 11, pp. 2514-2525, Nov. 2018
5
+ doi: 10.1109/TMI.2018.2837502
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2
+
3
+ O. Bernard, A. Lalande, C. Zotti, F. Cervenansky, et al.
4
+ "Deep Learning Techniques for Automatic MRI Cardiac Multi-structures Segmentation and Diagnosis: Is the Problem Solved ?" in IEEE Transactions on Medical Imaging, vol. 37, no. 11, pp. 2514-2525, Nov. 2018
5
+ doi: 10.1109/TMI.2018.2837502
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2
+
3
+ O. Bernard, A. Lalande, C. Zotti, F. Cervenansky, et al.
4
+ "Deep Learning Techniques for Automatic MRI Cardiac Multi-structures Segmentation and Diagnosis: Is the Problem Solved ?" in IEEE Transactions on Medical Imaging, vol. 37, no. 11, pp. 2514-2525, Nov. 2018
5
+ doi: 10.1109/TMI.2018.2837502
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1
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2
+
3
+ O. Bernard, A. Lalande, C. Zotti, F. Cervenansky, et al.
4
+ "Deep Learning Techniques for Automatic MRI Cardiac Multi-structures Segmentation and Diagnosis: Is the Problem Solved ?" in IEEE Transactions on Medical Imaging, vol. 37, no. 11, pp. 2514-2525, Nov. 2018
5
+ doi: 10.1109/TMI.2018.2837502
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1
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2
+
3
+ O. Bernard, A. Lalande, C. Zotti, F. Cervenansky, et al.
4
+ "Deep Learning Techniques for Automatic MRI Cardiac Multi-structures Segmentation and Diagnosis: Is the Problem Solved ?" in IEEE Transactions on Medical Imaging, vol. 37, no. 11, pp. 2514-2525, Nov. 2018
5
+ doi: 10.1109/TMI.2018.2837502
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1
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2
+
3
+ O. Bernard, A. Lalande, C. Zotti, F. Cervenansky, et al.
4
+ "Deep Learning Techniques for Automatic MRI Cardiac Multi-structures Segmentation and Diagnosis: Is the Problem Solved ?" in IEEE Transactions on Medical Imaging, vol. 37, no. 11, pp. 2514-2525, Nov. 2018
5
+ doi: 10.1109/TMI.2018.2837502
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2
+
3
+ O. Bernard, A. Lalande, C. Zotti, F. Cervenansky, et al.
4
+ "Deep Learning Techniques for Automatic MRI Cardiac Multi-structures Segmentation and Diagnosis: Is the Problem Solved ?" in IEEE Transactions on Medical Imaging, vol. 37, no. 11, pp. 2514-2525, Nov. 2018
5
+ doi: 10.1109/TMI.2018.2837502
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2
+
3
+ O. Bernard, A. Lalande, C. Zotti, F. Cervenansky, et al.
4
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