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Amshaker / unetr_plus_plus

[IEEE TMI-2024] UNETR++: Delving into Efficient and Accurate 3D Medical Image Segmentation
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about acdc #46

Closed smanman closed 1 year ago

smanman commented 1 year ago

Disturbed the author! I used the ACDC dataset you provided, trained 1000epoch, and found that the validation set results in summary.json in the validation_raw_postprocessed file and the predict_simple.py file I re-executed with the trained modelbest.model to generate predictive test labels inference acdc.py the results are different, in the second way my accuracy is only 0.02, the result is a bit outrageous, I want to ask you, where is the problem? Thank you so much! Here are the results of my experiment. (1) summary.json result: "reference": "/root/autodl-tmp/data/DATASET/nnFormer_preprocessed/Task001_ACDC/gt_segmentations/patient095_frame12.nii.gz", "test": "/root/autodl-tmp/data/DATASET/nnFormer_trained_models/unetr_pp/3d_fullres/Task001_ACDC/unetr_pp_trainer_acdc__unetr_pp_Plansv2.1/fold_0/validation_raw_postprocessed/patient095_frame12.nii.gz" } ], "mean": { "1": { "Accuracy": 0.9956343624672263, "Dice": 0.8133244859950842, "False Discovery Rate": 0.29189203000206926, "False Negative Rate": 0.023254209549772958, "False Omission Rate": 0.00016207729197368435, "False Positive Rate": 0.004265137268728636, "Jaccard": 0.6985343189273674, "Negative Predictive Value": 0.9998379227080264, "Precision": 0.7081079699979307, "Recall": 0.9767457904502269, "Total Positives Reference": 6604.7, "Total Positives Test": 8687.0, "True Negative Rate": 0.9957348627312712 }, "2": { "Accuracy": 0.995435524571116, "Dice": 0.8299434282979716, "False Discovery Rate": 0.1963606665798471, "False Negative Rate": 0.1402798206193858, "False Omission Rate": 0.0018131184462030017, "False Positive Rate": 0.00281533126728819, "Jaccard": 0.7109718398988019, "Negative Predictive Value": 0.998186881553797, "Precision": 0.8036393334201529, "Recall": 0.8597201793806143, "Total Positives Reference": 6715.075, "Total Positives Test": 7230.4, "True Negative Rate": 0.9971846687327117 }, "3": { "Accuracy": 0.9984309371979455, "Dice": 0.9426565408123958, "False Discovery Rate": 0.10098973894673105, "False Negative Rate": 0.006893134954023464, "False Omission Rate": 0.0001216667757356525, "False Positive Rate": 0.001473658952147136, "Jaccard": 0.8932048015679367, "Negative Predictive Value": 0.9998783332242642, "Precision": 0.899010261053269, "Recall": 0.9931068650459765, "Total Positives Reference": 8219.25, "Total Positives Test": 8895.475, "True Negative Rate": 0.9985263410478528 } } }, (2) Method 2 dice_pre.txt result:

patient002_frame01.nii.gz hd_rv: 82.2922 hd_myo: 108.1219 hd_lv: 106.4815

patient002_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0204 Dice_lv: 0.0523 hd_rv: 82.2922 hd_myo: 108.1219 hd_lv: 106.4815

patient002_frame12.nii.gz hd_rv: 177.4035 hd_myo: 114.3724 hd_lv: 112.4375

patient002_frame12.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0103 Dice_lv: 0.0641 hd_rv: 177.4035 hd_myo: 114.3724 hd_lv: 112.4375

patient003_frame01.nii.gz hd_rv: 109.4372 hd_myo: 110.0000 hd_lv: 88.5641

patient003_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0209 Dice_lv: 0.0385 hd_rv: 109.4372 hd_myo: 110.0000 hd_lv: 88.5641

patient003_frame15.nii.gz hd_rv: 107.0794 hd_myo: 110.8569 hd_lv: 91.2483

patient003_frame15.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0328 Dice_lv: 0.0433 hd_rv: 107.0794 hd_myo: 110.8569 hd_lv: 91.2483

patient008_frame01.nii.gz hd_rv: 65.2821 hd_myo: 73.0274 hd_lv: 111.9013

patient008_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0128 Dice_lv: 0.0000 hd_rv: 65.2821 hd_myo: 73.0274 hd_lv: 111.9013

patient008_frame13.nii.gz hd_rv: 62.0322 hd_myo: 74.6753 hd_lv: 112.2854

patient008_frame13.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0027 Dice_lv: 0.0000 hd_rv: 62.0322 hd_myo: 74.6753 hd_lv: 112.2854

patient009_frame01.nii.gz hd_rv: 91.6510 hd_myo: 80.1857 hd_lv: 97.2528

patient009_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0273 Dice_lv: 0.0263 hd_rv: 91.6510 hd_myo: 80.1857 hd_lv: 97.2528

patient009_frame13.nii.gz hd_rv: 68.1337 hd_myo: 76.5692 hd_lv: 100.3444

patient009_frame13.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0538 Dice_lv: 0.0401 hd_rv: 68.1337 hd_myo: 76.5692 hd_lv: 100.3444

patient012_frame01.nii.gz hd_rv: 67.4722 hd_myo: 99.8677 hd_lv: 100.7720

patient012_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0052 Dice_lv: 0.0148 hd_rv: 67.4722 hd_myo: 99.8677 hd_lv: 100.7720

patient012_frame13.nii.gz hd_rv: 61.6141 hd_myo: 102.4920 hd_lv: 101.1046

patient012_frame13.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0169 Dice_lv: 0.0550 hd_rv: 61.6141 hd_myo: 102.4920 hd_lv: 101.1046

patient014_frame01.nii.gz hd_rv: 41.8999 hd_myo: 92.3797 hd_lv: 76.6825

patient014_frame01.nii.gz Dice_rv: 0.0059 Dice_myo: 0.0189 Dice_lv: 0.0392 hd_rv: 41.8999 hd_myo: 92.3797 hd_lv: 76.6825

patient014_frame13.nii.gz hd_rv: 37.2424 hd_myo: 93.0261 hd_lv: 82.4742

patient014_frame13.nii.gz Dice_rv: 0.0073 Dice_myo: 0.0292 Dice_lv: 0.0201 hd_rv: 37.2424 hd_myo: 93.0261 hd_lv: 82.4742

patient017_frame01.nii.gz hd_rv: 75.0626 hd_myo: 89.7352 hd_lv: 104.4079

patient017_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0029 Dice_lv: 0.0060 hd_rv: 75.0626 hd_myo: 89.7352 hd_lv: 104.4079

patient017_frame09.nii.gz hd_rv: 73.0007 hd_myo: 93.9683 hd_lv: 108.6508

patient017_frame09.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0073 Dice_lv: 0.0022 hd_rv: 73.0007 hd_myo: 93.9683 hd_lv: 108.6508

patient024_frame01.nii.gz hd_rv: 68.4792 hd_myo: 90.4135 hd_lv: 107.5407

patient024_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0514 Dice_lv: 0.0057 hd_rv: 68.4792 hd_myo: 90.4135 hd_lv: 107.5407

patient024_frame09.nii.gz hd_rv: 33.6155 hd_myo: 95.4018 hd_lv: 113.2961

patient024_frame09.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0018 Dice_lv: 0.0135 hd_rv: 33.6155 hd_myo: 95.4018 hd_lv: 113.2961

patient042_frame01.nii.gz hd_rv: 69.6419 hd_myo: 120.7951 hd_lv: 110.6097

patient042_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0000 Dice_lv: 0.0229 hd_rv: 69.6419 hd_myo: 120.7951 hd_lv: 110.6097

patient042_frame16.nii.gz hd_rv: 57.1034 hd_myo: 120.7442 hd_lv: 114.2650

patient042_frame16.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0000 Dice_lv: 0.0531 hd_rv: 57.1034 hd_myo: 120.7442 hd_lv: 114.2650

patient048_frame01.nii.gz hd_rv: 66.6059 hd_myo: 81.9582 hd_lv: 105.7329

patient048_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0003 Dice_lv: 0.0477 hd_rv: 66.6059 hd_myo: 81.9582 hd_lv: 105.7329

patient048_frame08.nii.gz hd_rv: 65.4458 hd_myo: 83.0602 hd_lv: 112.8105

patient048_frame08.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0046 Dice_lv: 0.0126 hd_rv: 65.4458 hd_myo: 83.0602 hd_lv: 112.8105

patient049_frame01.nii.gz hd_rv: 53.1644 hd_myo: 89.5637 hd_lv: 128.9333

patient049_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0430 Dice_lv: 0.0313 hd_rv: 53.1644 hd_myo: 89.5637 hd_lv: 128.9333

patient049_frame11.nii.gz hd_rv: 101.0940 hd_myo: 92.1358 hd_lv: 131.3324

patient049_frame11.nii.gz Dice_rv: 0.0013 Dice_myo: 0.0188 Dice_lv: 0.0380 hd_rv: 101.0940 hd_myo: 92.1358 hd_lv: 131.3324

patient053_frame01.nii.gz hd_rv: 122.7467 hd_myo: 96.3878 hd_lv: 127.2360

patient053_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0728 Dice_lv: 0.0079 hd_rv: 122.7467 hd_myo: 96.3878 hd_lv: 127.2360

patient053_frame12.nii.gz hd_rv: 122.7096 hd_myo: 98.8683 hd_lv: 133.4103

patient053_frame12.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0022 Dice_lv: 0.0090 hd_rv: 122.7096 hd_myo: 98.8683 hd_lv: 133.4103

patient055_frame01.nii.gz hd_rv: 114.0702 hd_myo: 103.0825 hd_lv: 102.4353

patient055_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0032 Dice_lv: 0.0117 hd_rv: 114.0702 hd_myo: 103.0825 hd_lv: 102.4353

patient055_frame10.nii.gz hd_rv: 47.6707 hd_myo: 107.0091 hd_lv: 105.7852

patient055_frame10.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0055 Dice_lv: 0.0000 hd_rv: 47.6707 hd_myo: 107.0091 hd_lv: 105.7852

patient064_frame01.nii.gz hd_rv: 74.9667 hd_myo: 107.5156 hd_lv: 114.1464

patient064_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0124 Dice_lv: 0.0682 hd_rv: 74.9667 hd_myo: 107.5156 hd_lv: 114.1464

patient064_frame12.nii.gz hd_rv: 68.7677 hd_myo: 109.0431 hd_lv: 117.1108

patient064_frame12.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0351 Dice_lv: 0.0673 hd_rv: 68.7677 hd_myo: 109.0431 hd_lv: 117.1108

patient067_frame01.nii.gz hd_rv: 67.9412 hd_myo: 100.1714 hd_lv: 101.1200

patient067_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0353 Dice_lv: 0.1424 hd_rv: 67.9412 hd_myo: 100.1714 hd_lv: 101.1200

patient067_frame10.nii.gz hd_rv: 67.9412 hd_myo: 103.9519 hd_lv: 99.0656

patient067_frame10.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0799 Dice_lv: 0.1669 hd_rv: 67.9412 hd_myo: 103.9519 hd_lv: 99.0656

patient079_frame01.nii.gz hd_rv: 80.4301 hd_myo: 121.6643 hd_lv: 112.8273

patient079_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0378 Dice_lv: 0.0234 hd_rv: 80.4301 hd_myo: 121.6643 hd_lv: 112.8273

patient079_frame11.nii.gz hd_rv: 51.3936 hd_myo: 127.2053 hd_lv: 123.0197

patient079_frame11.nii.gz Dice_rv: 0.0006 Dice_myo: 0.0086 Dice_lv: 0.0444 hd_rv: 51.3936 hd_myo: 127.2053 hd_lv: 123.0197

patient081_frame01.nii.gz hd_rv: 71.5612 hd_myo: 95.4125 hd_lv: 99.2824

patient081_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0041 Dice_lv: 0.0053 hd_rv: 71.5612 hd_myo: 95.4125 hd_lv: 99.2824

patient081_frame07.nii.gz hd_rv: 51.4451 hd_myo: 97.0000 hd_lv: 103.8220

patient081_frame07.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0085 Dice_lv: 0.0018 hd_rv: 51.4451 hd_myo: 97.0000 hd_lv: 103.8220

patient088_frame01.nii.gz hd_rv: 60.8169 hd_myo: 99.6218 hd_lv: 93.9191

patient088_frame01.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0000 Dice_lv: 0.0135 hd_rv: 60.8169 hd_myo: 99.6218 hd_lv: 93.9191

patient088_frame12.nii.gz hd_rv: 27.4773 hd_myo: 100.9121 hd_lv: 100.0620

patient088_frame12.nii.gz Dice_rv: 0.0000 Dice_myo: 0.0000 Dice_lv: 0.0031 hd_rv: 27.4773 hd_myo: 100.9121 hd_lv: 100.0620

patient092_frame01.nii.gz hd_rv: 19.0526 hd_myo: 78.1521 hd_lv: 103.9016

patient092_frame01.nii.gz Dice_rv: 0.0077 Dice_myo: 0.0209 Dice_lv: 0.0439 hd_rv: 19.0526 hd_myo: 78.1521 hd_lv: 103.9016

patient092_frame06.nii.gz hd_rv: 21.5430 hd_myo: 76.9571 hd_lv: 107.2476

patient092_frame06.nii.gz Dice_rv: 0.0250 Dice_myo: 0.1117 Dice_lv: 0.0654 hd_rv: 21.5430 hd_myo: 76.9571 hd_lv: 107.2476

patient095_frame01.nii.gz hd_rv: 23.3463 hd_myo: 36.8170 hd_lv: 106.4070

patient095_frame01.nii.gz Dice_rv: 0.0039 Dice_myo: 0.0014 Dice_lv: 0.0530 hd_rv: 23.3463 hd_myo: 36.8170 hd_lv: 106.4070

patient095_frame12.nii.gz hd_rv: 30.2655 hd_myo: 29.3019 hd_lv: 112.3871

patient095_frame12.nii.gz Dice_rv: 0.0076 Dice_myo: 0.2153 Dice_lv: 0.1232 hd_rv: 30.2655 hd_myo: 29.3019 hd_lv: 112.3871

Mean_Dice Dice_rv0.0014833411610974427 Dice_myo0.025901555917205978 Dice_lv0.036925817218667785 Mean_HD HD_rv68.9724658656119 HD_myo94.56059658967824 HD_lv107.05783058276431

avg_hd:90.19696434601815 DSC:0.02143690476565707 HD:90.19696434601815

Amshaker commented 1 year ago

I am not sure what is the problem in your code. You can simply report the results you got in the validation set results of summary.json in the validation_raw_postprocessed folder. Both are correct.