upload to new server
This commit is contained in:
Furen
parent
262c94be2d
commit
7cfd15c6c3
160 changed files with 9431 additions and 606 deletions
986
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./2-infer.py /nn/7091925/20230208/CT/9 /nn/7091925/20230208/MR/7
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./1-move.py 6035638
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./2-infer.py /nn/5695691/20230216/CT/a /nn/5695691/20230216/MR/7
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./2-infer.py /nn/7123316/20230220/CT/9 /nn/7123316/20230220/MR/7
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./2-infer.py /nn/5831210/20230220/CT/c /nn/5831210/20230220/MR/a
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./1-move.py 3387187
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./2-infer.py /nn/3387187/20230221/CT/a /nn/3387187/20230221/MR/7
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./1-move.py 6803836
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./2-infer.py /nn/6803836/20230221/CT/10 /nn/6803836/20230221/MR/e
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./1-move.py
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./2-infer.py /nn/6466293/20230222/CT/a /nn/6466293/20230222/MR/7
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./1-move.py 4607357
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./2-infer.py /nn/4607357/20230224/CT/a /nn/4607357/20230224/MR/7
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./2-infer.py /nn/7055212/20230224/CT/9 /nn/7055212/20230224/MR/7
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./1-move.py 5027429
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./2-infer.py /nn/5027429/20230306/CT/b /nn/5027429/20230306/MR/9
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./1-move.py 7123530
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./2-infer.py /nn/7123530/20230307/CT/a /nn/7123530/20230307/MR/7
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./2-infer.py /nn/7130932/20230307/CT/a /nn/7130932/20230307/MR/7
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./1-move.py 5771396
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./2-infer.py /nn/5771396/20230308/CT/a /nn/5771396/20230308/MR/7
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./1-move.py 7128131
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./2-infer.py /nn/7128131/20230310/CT/a /nn/7128131/20230310/MR/7
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./1-move.py 6412311
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./2-infer.py /nn/6412311/20230313/CT/9 /nn/6412311/20230313/MR/7
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./1-move.py
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./2-infer.py /nn/5494530/20230313/CT/a /nn/5494530/20230313/MR/7
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./1-move.py 7128706
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./2-infer.py /nn/7128706/20230310/CT/c /nn/7128706/20230310/MR
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./1-move.py 6925186
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./2-infer.py /nn/6925186/20230314/CT/a /nn/6925186/20230314/MR/7
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./1-move.py 3863530
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./1-move.py 3863530
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./2-infer.py /nn/3863530/20230314/CT/a /nn/3863530/20230314/MR/7
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./1-move.py 7131041
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./2-infer.py /nn/7131041/20230315/CT/a /nn/7131041/20230315/MR/7
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./1-move.py 5682089
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./2-infer.py /nn/5682089/20230315/CT/a /nn/5682089/20230315/MR/7
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./1-move.py 5553220
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./1-move.py 3589548
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./2-infer.py /nn/3589548/20230317/CT/9 /nn/3589548/20230317/MR/7
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./1-move.py 2111161
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./2-infer.py /nn/2111161/20230317/CT/9 /nn/2111161/20230317/MR/7
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./1-move.py 6167673
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./2-infer.py /nn/6167673/20230320/CT/9 /nn/6167673/20230320/MR/7
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./1-move.py 2372501
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./2-infer.py /nn/2372501/20230320/CT/c /nn/2372501/20230320/MR/2
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./1-move.py 7134146
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./2-infer.py /nn/7134146/20230321/CT/a /nn/7134146/20230321/MR/7
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./1-move.py 6017134
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./2-infer.py /nn/6017134/20230321/CT/9 /nn/6017134/20230321/MR/7
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./1-move.py 5061967
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./2-infer.py /nn/5061967/20230322/CT/b /nn/5061967/20230322/MR/8
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./1-move.py 3060758
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./2-infer.py /nn/3060758/20230322/CT/a /nn/3060758/20230322/MR/7
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./1-move.py 6943475
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./2-infer.py /nn/6943475/20230323/CT/9 /nn/6943475/20230323/MR/7
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./1-move.py 5027838
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./2-infer.py /nn/5027838/20230323/CT/a /nn/5027838/20230323/MR/7
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./1-move.py 6783185
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./2-infer.py /nn/6783185/20230324/CT/a /nn/6783185/20230324/MR/7
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./1-move.py 4482158
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./2-infer.py /nn/4482158/20230324/CT/9 /nn/4482158/20230324/MR/7
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ls /nn
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ls -ltr /nn
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ls
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./1-move.py 4482158
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./1-move.py 6764185
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./2-infer.py /nn/6764185/20230327/CT/9 /nn/6764185/20230327/MR/7
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./1-move.py
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./2-infer.py /nn/7127857/20230327/CT/a /nn/7127857/20230327/MR/7
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./1-move.py 6553099
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./2-infer.py /nn/6553099/20230328/CT/9 /nn/6553099/20230328/MR/7
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./1-move.py 7040640
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./2-infer.py /nn/7040640/20230328/CT/a /nn/7040640/20230328/MR/7
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./1-move.py 6553099
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./2-infer.py /nn/6553099/20230328/CT/9 /nn/6553099/20230328/MR/7
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./1-move.py 7106897
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./2-infer.py /nn/7106897/20230329/CT/a /nn/7106897/20230329/MR/7
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./1-move.py 5261092
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./2-infer.py /nn/5261092/20230329/CT/a /nn/5261092/20230329/MR/7
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./1-move.py 4301162
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./2-infer.py /nn/4301162/20230330/CT/d /nn/4301162/20230330/MR/7
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./1-move.py 7131077
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python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
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python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
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export nnUNet_results=/123/onlylian/nnUNet_results
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export nnUNet_preprocessed=/123/onlylian/nnUNet_preprocessed
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export nnUNet_results=/123/onlylian/nnUNet_results
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cd /123/onlylian/nnUNet_results
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ls -l
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ls -l Dataset505
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python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
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cd ..
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python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
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python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
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export nnUNet_raw="/onlylian/nnUNet_raw"
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export nnUNet_preprocessed="/onlylian/nnUNet_preprocessed"
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export nnUNet_results="/onlylian/nnUNet_results"
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echo $nnUNet_raw
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echo $nnUNet_preprocessed
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echo $nnUNet_results
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nnUNetv2_predict -i /nn/7208298/20241213/input -o /nn/7208298/20241213/output -d 505 -c 3d_fullres -f 0 -tr nnUNetTrainer -p nnUNetPlans --checkpoint /onlylian/nnUNet_results/Dataset505/nnUNetTrainer__nnUNetPlans__3d_fullres/fold_0/checkpoint_final.pth
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nnUNetv2_predict -i /nn/7208298/20241213/input -o /nn/7208298/20241213/output -d 505 -c 3d_fullres -f 0 -tr nnUNetTrainer -p nnUNetPlans
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ls -l /onlylian/nnUNet_results
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ls -l /onlylian/nnUNet_raw
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python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
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/nn/7208298/20241213/output
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ls -l /nn/7208298/20241213/output
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cat /nn/7208298/20241213/output/[filename]
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cp -r /nn/7208298/20241213/output ./onlylian
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cp -r /nn/7208298/20241213/output ./onlylian
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cp -r /nn/7208298/20241213/input ./onlylian
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./1-move.py 6996427
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./1-move.py 6996427
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./2-infer.py /nn/6996427/20230331/CT/a /nn/6996427/20230331/MR/7
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python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
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cp -r /nn/7208298/20241213/output ./onlylian
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python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
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cp -r /nn/7208298/20241213/output ./onlylian
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python3 oar.py /nn/2783853/20241217/CT/9 /nn/2783853/20241217/MR/8
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python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
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cp -r /nn/7208298/20241213/output ./onlylian
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python3 oar.py /nn/2783853/20241217/CT/9 /nn/2783853/20241217/MR/
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python3 oar.py /nn/4608443/20241219/CT/a /nn/4608443/20241219/MR/7
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python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
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cp -r /nn/7208298/20241213/output ./onlylian
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python3 oar.py /nn/5108920/20241223/CT/a /nn/5108920/20241223/MR/7
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python3 oar.py /nn/5435462/20241224/CT/9 /nn/5435462/20241224/MR/7
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python3 oar.py /nn/2944822/20241224/CT/e /nn/2944822/20241224/MR/9
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python3 oar.py /nn/7287366/20241225/CT/9 /nn/7287366/20241225/MR/7
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python3 oar.py /nn/6405610/20241225/CT/9 /nn/6405610/20241225/MR/7
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python3 oar.py /nn/7286032/20241226/CT/b /nn/7286032/20241226/MR/9
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python3 oar.py /nn/1786330/20241226/CT/b /nn/1786330/20241226/MR/8
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python3 oar.py /nn/7284108/20241227/CT/b /nn/7284108/20241227/MR/8
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python3 oar.py /nn/4365592/20241227/CT/a /nn/4365592/20241227/MR/7
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python3 oar.py /nn/2367245/20241223/CT/b /nn/2367245/20241231/MR/7
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python3 oar.py /nn/3018505/20250102/CT/9 /nn/3018505/20250102/MR/8
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python3 oar.py /nn/6827885/20250102/CT/a /nn/6827885/20250102/MR/7
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python3 oar.py /nn/2556090/20250103/CT/a /nn/2556090/20250103/MR/7
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python3 oar.py /nn/6902522/20250103/CT/a /nn/6902522/20250103/MR/7
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python3 oar.py /nn/5908183/20250106/CT/a /nn/5908183/20250106/MR/7
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python3 oar.py /nn/7165972/20250106/CT/a /nn/7165972/20250106/MR/7
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python3 oar.py /nn/6248872/20250108/CT/a /nn/6248872/20250108/MR/8
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python3 oar.py /nn/7223127/20250108/CT/a /nn/7223127/20250108/MR/6
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python3 oar.py /nn/4398001/20250114/CT/9 /nn/4398001/20250114/MR/7
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python3 oar.py /nn/4003636/20250114/CT/9 /nn/4003636/20250114/MR/8
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python3 oar.py /nn/5131302/20250116/CT/9 /nn/5131302/20250116/MR/7
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python3 oar.py /nn/5337151/20250116/CT/9 /nn/5337151/20250103/MR/b
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python3 oar.py /nn/7283904/20250116/CT/9 /nn/7283904/20250116/MR/7
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python3 oar.py /nn/5517865/20250117/CT/a /nn/5517865/20250117/MR/8
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python3 oar.py /nn/7231788/20250120/CT/a /nn/7231788/20250120/MR/8
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python3 oar.py /nn/3427537/20250120/CT/a /nn/3427537/20250120/MR/8
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python3 oar.py /nn/7154553/20250122/CT/9 /nn/7154553/20250122/MR/7
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python3 oar.py /nn/7239152/20250124/CT/a /nn/7239152/20250124/MR/7
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python3 oar.py /nn/2957658/20250124/CT/b /nn/2957658/20250124/MR/8
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python3 oar.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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python3 oar.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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python3 oar.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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conda env list
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ls -l
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python oar.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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./1-move.py 4608443
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./1-move.py 1561614
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./2-infer.py /nn/1561614/20230331/CT/b /nn/1561614/20230331/MR/8
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top
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exit
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./1-move.py
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./2-infer.py /nn/6623737/20230406/CT/8 /nn/6623737/20230406/MR/7
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./1-move.py 6631848
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./2-infer.py /nn/6631848/20220810/CT/9 /nn/6631848/20230406/MR/7
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./1-move.py 6631848
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./2-infer.py /nn/6631848/20230406/CT/a /nn/6631848/20230406/MR/7
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./2-infer.py /nn/6631848/20230406/CT/a /nn/6631848/20230406/MR/7
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./2-infer.py /nn/6631848/20230406/CT/a /nn/6631848/20230406/MR/7
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./2-infer.py /nn/6631848/20230406/CT/a /nn/6631848/20230406/MR/7
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./2-infer.py /nn/6631848/20230406/CT/a /nn/6631848/20230406/MR/7
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./1-move.py 6418004
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./2-infer.py /nn/8045956/20230407/CT/b /nn/8045956/20230407/MR/7
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./2-infer.py /nn/6418004/20230407/CT/8 /nn/6418004/20230407/MR/7
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./2-infer.py /nn/2644799/20230410/CT/a /nn/2644799/20230410/MR/7
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./1-move.py 4572736
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./1-move.py 5767800
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./1-move.py 5760888
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./1-move.py 6700596
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./2-infer.py /nn/6700596/20230418/CT/9 /nn/6700596/20230418/MR/7
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./1-move.py 2334044
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./2-infer.py /nn/2334044/20230419/CT/9 /nn/2334044/20230419/MR/7
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./1-move.py 3001393
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./1-move.py 3001393
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||||
./2-infer.py /nn/4118618/20230714/CT/d /nn/4118618/20230714/MR/8
|
||||
./1-move.py 7138156
|
||||
./2-infer.py /nn/7138156/20230714/CT/9 /nn/7138156/20230714/MR/7
|
||||
22444455555555444444./1-move.py 14444454555
|
||||
./1-move.py 4214975
|
||||
./2-infer.py /nn/4214975/20230717/CT/c /nn/4214975/20230717/MR/8
|
||||
./1-move.py 3485443
|
||||
./2-infer.py /nn/3485443/20230717/CT/a /nn/3485443/20230717/MR/7
|
||||
./1-move.py 6824186
|
||||
./2-infer.py /nn/6824186/20230718/CT/9 /nn/6824186/20230718/MR/7
|
||||
./1-move.py 6547497
|
||||
./2-infer.py /nn/6547497/20230718/CT/8 /nn/6547497/20230718/MR/7
|
||||
./1-move.py 1875185
|
||||
./2-infer.py /nn/1875185/20230719/CT/a /nn/1875185/20230719/MR/6
|
||||
./1-move.py 7023789
|
||||
./2-infer.py /nn/7023789/20230719/CT/a /nn/7023789/20230719/MR/6
|
||||
./1-move.py 2098952
|
||||
./2-infer.py /nn/2098952/20230720/CT/a /nn/2098952/20230720/MR/6
|
||||
./1-move.py 7151783
|
||||
./2-infer.py /nn/7151783/20230720/CT/a /nn/7151783/20230720/MR/7
|
||||
./1-move.py 7075650
|
||||
./2-infer.py /nn/7075650/20230721/CT/9 /nn/7075650/20230721/MR/7
|
||||
./1-move.py 4352680
|
||||
./2-infer.py /nn/4352680/20230721/CT/9 MAR
|
||||
./2-infer.py /nn/4352680/20230721/CT/9 MAR /nn/4352680/20230721/MR/7
|
||||
./1-move.py 4352680
|
||||
./2-infer.py /nn/4352680/20230721/CT/a /nn/4352680/20230721/MR/7
|
||||
./1-move.py 7144639
|
||||
./2-infer.py /nn/7144639/20230724/CT/a /nn/7144639/20230724/MR/3
|
||||
./1-move.py 4505405
|
||||
./2-infer.py /nn/4505405/20230724/CT/9 /nn/4505405/20230724/MR/7
|
||||
./1-move.py 7157433
|
||||
./2-infer.py /nn/7157433/20230725/CT/b /nn/7157433/20230725/MR/7
|
||||
./1-move.py 3283427
|
||||
./2-infer.py /nn/3283427/20230725/CT/9 /nn/3283427/20230725/MR/7
|
||||
./1-move.py 6401745
|
||||
./2-infer.py /nn/6401745/20230726/CT/a /nn/6401745/20230726/MR/6
|
||||
./1-move.py 4383470
|
||||
./2-infer.py /nn/4383470
|
||||
./1-move.py 1994335
|
||||
./2-infer.py /nn/1994335/20230727/CT/9 /nn/1994335/20230727/MR/7
|
||||
./1-move.py 6184547
|
||||
./2-infer.py /nn/6184547/20230728/CT/a /nn/6184547/20230728/MR/7
|
||||
./1-move.py 5223617
|
||||
./2-infer.py /nn/5223617/20220520/CT/8 /nn/5223617/20230728/MR/7
|
||||
./1-move.py /nn/5223617/20230728/MR/7
|
||||
|
||||
./1-move.py 5223617
|
||||
./1-move.py /nn/5223617/20230728/CT/8 /nn/5223617/20230728/MR/7
|
||||
./1-move.py /nn/5223617/20230728/CT/8 /nn/5223617/20230728/MR/7
|
||||
./2-infer.py /nn/5223617/20220520/CT/8 /nn/5223617/20230728/MR/7
|
||||
./1-move.py 1003532
|
||||
./2-infer.py /nn/1003532/20230728/CT/9 /nn/1003532/20230728/MR/2
|
||||
./1-move.py 5223617
|
||||
./2-infer.py /nn/5223617/20230728/CT/8 /nn/5223617/20230728/MR/7
|
||||
./1-move.py 3307080
|
||||
./2-infer.py /nn/3307080/20230731/CT/8 /nn/3307080/20230731/MR/7
|
||||
./1-move.py 3307080
|
||||
./2-infer.py /nn/3307080/20230731/CT/8 /nn/3307080/20230731/MR/7
|
||||
./1-move.py 2431392
|
||||
./2-infer.py /nn/2431392/20230731/CT/9 /nn/2431392/20230731/MR/2
|
||||
./1-move.py 7155758
|
||||
./2-infer.py /nn/7155758/20230801/CT/a /nn/7155758/20230801/MR/7
|
||||
./1-move.py 5879999
|
||||
./2-infer.py /nn/5879999/20230801/CT/a /nn/5879999/20230801/MR/7
|
||||
./1-move.py 6460676
|
||||
./2-infer.py /nn/6460676/20230802/CT/9 /nn/6460676/20230802/MR/7
|
||||
./1-move.py 4107788
|
||||
./2-infer.py /nn/4107788/20230802/CT/a /nn/4107788/20230802/MR/7
|
||||
./1-move.py 7159471
|
||||
./2-infer.py /nn/7159471/20
|
||||
./1-move.py 7159471
|
||||
./2-infer.py /nn/7159471/20230804/CT/a /nn/7159471/20230804/MR/7
|
||||
ps aux
|
||||
ps aux
|
||||
ps aux
|
||||
./1-move.py 7239182
|
||||
./2-infer.py /nn/7239182/20250107/CT/8 /nn/7239182/20250107/MR/7
|
||||
./1-move.py 6248872
|
||||
./2-infer.py /nn/6248872/20250108/CT/a /nn/6248872/20250108/MR/8
|
||||
./1-move.py 7223127
|
||||
./1-move.py 1918501
|
||||
./2-infer.py /nn/1918501/20250109/CT/a /nn/1918501/20250109/MR/8
|
||||
./1-move.py 8049454
|
||||
./2-infer.py /nn/8049454/20250109/CT/9 /nn/8049454/20250109/MR/8
|
||||
./1-move.py A105575
|
||||
./1-move.py 6217784
|
||||
./2-infer.py /nn/6217784/20250110/CT/2 /nn/A105575/20250107/MR/8
|
||||
./1-move.py 6736489
|
||||
./2-infer.py /nn/6736489/20250110/CT/a /nn/6736489/20250110/MR/8
|
||||
./1-move.py 6052644
|
||||
./2-infer.py /nn/6052644/20250110/CT/b /nn/6052644/20250110/MR/9
|
||||
./1-move.py 6052644
|
||||
./2-infer.py /nn/6052644/20250110/CT/b /nn/6052644/20250110/MR/9
|
||||
./1-move.py 2516940
|
||||
./2-infer.py /nn/2516940/20250113/CT/a /nn/2516940/20250113/MR/7
|
||||
./1-move.py 7190177
|
||||
./2-infer.py /nn/7190177/20250113/CT/b /nn/7190177/20250113/MR/8
|
||||
./1-move.py 4398001
|
||||
./1-move.py 4003636
|
||||
./1-move.py 7233916
|
||||
./2-infer.py /nn/7233916/20250115/CT/b /nn/7233916/20250115/MR/7
|
||||
./1-move.py 7295438
|
||||
./2-infer.py /nn/7295438/20250115/CT/d /nn/7295438/20250115/MR/9
|
||||
./1-move.py 5337151
|
||||
./1-move.py 5337151
|
||||
./1-move.py 5337151
|
||||
./1-move.py 5131302
|
||||
./1-move.py 5337151
|
||||
./1-move.py 7283904
|
||||
./1-move.py 4182983
|
||||
./2-infer.py /nn/4182983/20250117/CT/a /nn/4182983/20250117/MR/6
|
||||
./1-move.py 5517865
|
||||
./1-move.py 5517865
|
||||
./1-move.py 7283904
|
||||
./1-move.py 7231788
|
||||
./1-move.py 3427537
|
||||
./1-move.py 6449647
|
||||
./2-infer.py /nn/6449647/20250121/CT/8 /nn/6449647/20250121/MR/7
|
||||
./1-move.py 2508411
|
||||
./2-infer.py /nn/2508411/20250121/CT/c /nn/2508411/20250121/MR/9
|
||||
./1-move.py 7154553
|
||||
./1-move.py 7253850
|
||||
./2-infer.py /nn/7253850/20250123/CT/b /nn/7253850/20250123/MR/8
|
||||
./1-move.py 7240437
|
||||
./2-infer.py /nn/7240437/20250123/CT/a /nn/7240437/20250123/MR/8
|
||||
./1-move.py 7239152
|
||||
./1-move.py 2957658
|
||||
./1-move.py 7295866
|
||||
./2-infer.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
nvidia-smi
|
||||
nvidia-smi
|
||||
nvidia-smi
|
||||
cd onlylian/
|
||||
ls
|
||||
python3 oar.py /nn/7295866/20250127/CT/a /nn/72/nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
ls /nn
|
||||
python3 oar.py /nn/7295866/20250127/CT/a /nn/72/nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
copy oar.py oar2.py
|
||||
cp oar.py oar2.py
|
||||
dir /nn/7295866/
|
||||
dir /nn/7295866/20250127/
|
||||
dir /nn/7295866/20250127/nii/
|
||||
dir /nn/7295866/20250127/output/
|
||||
dir /nn/7295866/20250127/nii/
|
||||
dir /nn/7295866/20250127/input/
|
||||
dir /nn/7295866/20250127/output/
|
||||
dir /nn/7295866/20250127/CT/
|
||||
dir /nn/7295866/20250127/
|
||||
ls -lR /nn/7295866/20250127/
|
||||
cd onlylian/
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
ls /nn/7295866/20250127/output/processed_7_3D_SAG_T1_MPRAGE_+C_20250127132612.nii.gz
|
||||
ls /nn/7295866/20250127/output/processed_7_3D_SAG_T1_MPRAGE_+C_20250127132612.nii.gz
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
ls /nn/7295866/20250127/
|
||||
ls /nn/7295866/20250127/pyradise/
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
apt install libxrender1
|
||||
python test2.py
|
||||
python test2.py
|
||||
python test2.py
|
||||
ls /nn/7295866/20250127/
|
||||
ls /nn/7295866/20250127/CT/
|
||||
python test2.py
|
||||
ls /nn/7295866/20250127/CT/
|
||||
ls -l /nn/7295866/20250127/CT/
|
||||
ls
|
||||
ls -ltr
|
||||
copy oar.py oar2.py
|
||||
cp oar.py oar2.py
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
ls /nn/7295866/20250127/CT/
|
||||
ls -ltr /nn/7295866/20250127/CT/
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
ls -ltr /nn/7295866/20250127/CT/
|
||||
ls -ltr /nn/7295866/20250127/CT/a-rtss*
|
||||
rm -ltr /nn/7295866/20250127/CT/a-rtss*
|
||||
rm /nn/7295866/20250127/CT/a-rtss*
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
rm -ltr /nn/7295866/20250127/CT/a-rtss*
|
||||
rm -ltr /nn/7295866/20250127/CT/
|
||||
ls /nn/7295866/20250127/CT/
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
ls /nn/7295866/20250127/CT/
|
||||
ls /nn/7295866/20250127/CT/7295866/
|
||||
ls -l /nn/7295866/20250127/CT/7295866/
|
||||
ls -l /nn/7295866/20250127/pyradise/
|
||||
ls -l /nn/7295866/20250127/pyradise/7295866/
|
||||
rm -rf /nn/7295866/20250127/pyradise/
|
||||
rm -rf /nn/7295866/20250127/pyradise
|
||||
rm -rf /nn/7295866/20250127/CT/7295866
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
ls /nn/7295866/20250127/pyradise
|
||||
ls /nn/7295866/20250127/pyradise
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
/nn/7295866/20250127/pyradise
|
||||
ls /nn/7295866/20250127/pyradise
|
||||
ls /nn/7295866/20250127/
|
||||
ls /nn/7295866/20250127/seg
|
||||
rm -rf /nn/7295866/20250127/seg
|
||||
ls /nn/7295866/20250127/
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
ls /nn/7295866/20250127/CT/a-rtss.dcm
|
||||
ls /nn/7295866/20250127/pyradise/
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
cp oar2.py oar3.py
|
||||
cd registration
|
||||
ls
|
||||
python best_reg.py
|
||||
cd ..
|
||||
python registration/best_reg.py
|
||||
python -m registration.best_reg
|
||||
python -m registration.best_reg
|
||||
python -m registration.best_reg
|
||||
python -m registration.best_reg
|
||||
python -m registration.best_reg
|
||||
cd onlylian/
|
||||
ls
|
||||
python -m registration.best_reg
|
||||
python -m registration.best_reg
|
||||
python -m registration.best_reg
|
||||
ls '/nn/7295866/20250127/nii/7_3D_SAG_T1_MPRAGE_+C_20250127132612_100.nii.gz'
|
||||
ls '/nn/7295866/20250127/nii/a_1.1_CyberKnife_head(MAR)_20250127111447.label.nii.gz'
|
||||
python -m registration.best_reg
|
||||
python -m registration.best_reg
|
||||
python -m registration.best_reg
|
||||
ls /nn/7295866/20250127/pyradise
|
||||
rm -rf /nn/7295866/20250127/pyradise
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
ls nnUNet_results/Dataset222_OAR_TV/
|
||||
ls nnUNet_results/Dataset222_OAR_TV/nnUNetTrainer__nnUNetPlans__2d/
|
||||
ls nnUNet_results/Dataset222_OAR_TV/nnUNetTrainer__nnUNetPlans__2d/fold_0/
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
ls /nn/7295866/20250127/pyradise
|
||||
rm -rf /nn/7295866/20250127/pyradise
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
chmod 777 /nn/7295866/20250127/
|
||||
chmod 777 /nn/7295866/20250127/pyradise/
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
ls /nn/7295866/20250127/CT/a-rtss.dcm
|
||||
ping 172.16.40.36
|
||||
nnUNetv2_find_best_configuration
|
||||
export nnUNet_raw"/123/onlylian/nnUNet_raw"
|
||||
export nnUNet_raw="/123/onlylian/nnUNet_raw"
|
||||
export nnUNet_results="/123/onlylian/nnUNet_results"
|
||||
nnUNetv2_find_best_configuration 222
|
||||
export nnUNet_preprocessed="/123/onlylian/nnUNet_preprocessed"
|
||||
nnUNetv2_find_best_configuration 222
|
||||
python3
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
conda install conda-forge::niftyreg
|
||||
apt search niftyreg
|
||||
pip install fireants
|
||||
ps
|
||||
ps aux
|
||||
kill 8051
|
||||
git clone https://github.com/rohitrango/fireants
|
||||
rm -rf fireants/
|
||||
pip install git+https://github.com/rohitrango/fireants.git
|
||||
git clone https://github.com/rohitrango/fireants
|
||||
cd fireants/
|
||||
ls
|
||||
nano pyproject.toml
|
||||
pip install -e .
|
||||
pip --version
|
||||
pip install --upgrade pip
|
||||
pip install -e .
|
||||
ㄎcd
|
||||
cd
|
||||
cd onlylian/
|
||||
ls
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
nvidia-smi
|
||||
nvidia-smi
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
python -m registration.fireants_reg
|
||||
ls
|
||||
ls ~/0/
|
||||
ls ~/0/mri_synthmorph.zip
|
||||
unzip ~/0/mri_synthmorph.zip
|
||||
ls
|
||||
cd mri_synthmorph/
|
||||
ls
|
||||
conda
|
||||
conda list
|
||||
ls
|
||||
./mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz moving.nii.gz clipped.nii.gz -g
|
||||
chmod +x mri_synthmorph
|
||||
./mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz moving.nii.gz clipped.nii.gz -g
|
||||
python
|
||||
pip install git+https://github.com/adalca/neurite.git git+https://github.com/freesurfer/surfa.git git+https://github.com/voxelmorph/voxelmorph.git
|
||||
./mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz moving.nii.gz clipped.nii.gz -g
|
||||
conda list
|
||||
conda install tensorflow-gpu
|
||||
conda update conda
|
||||
conda update -n base conda
|
||||
conda install tensorflow-gpu
|
||||
conda install -n base conda-libmamba-solver
|
||||
conda config --set solver libmamba
|
||||
conda install -n base conda-libmamba-solver
|
||||
pip install --upgrade pip
|
||||
conda update -n base conda
|
||||
c
|
||||
pip install tensorflow-gpu
|
||||
./mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz moving.nii.gz clipped.nii.gz -g
|
||||
ls
|
||||
cd ..
|
||||
ls
|
||||
./mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz '/nn/7295866/20250127/output/processed_7_3D_SAG_T1_MPRAGE_+C_20250127132612.nii.gz'moving.nii.gz clipped.nii.gz -g
|
||||
./mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz '/nn/7295866/20250127/output/processed_7_3D_SAG_T1_MPRAGE_+C_20250127132612.nii.gz'moving.nii.gz clipped.nii.gz
|
||||
clear
|
||||
cd onlylian/
|
||||
ls
|
||||
mri_synthmorph/mri_synthmorph '/nn/7295866/20250127/output/processed_7_3D_SAG_T1_MPRAGE_+C_20250127132612.nii.gz' -m affine -t trans.lta -o out-aff.nii.gz moving.nii.gz clipped.nii.gz -g
|
||||
mri_synthmorph/mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz '/nn/7295866/20250127/nii/a_1.1_CyberKnife_head(MAR)_20250127111447_5.nii.gz' '/nn/7295866/20250127/nii/7_3D_SAG_T1_MPRAGE_+C_20250127132612_100.nii.gz' -g
|
||||
ls
|
||||
cd mri_synthmorph/
|
||||
ls
|
||||
mkdir models
|
||||
cd models/
|
||||
wget https://surfer.nmr.mgh.harvard.edu/docs/synthmorph/synthmorph.affine.2.h5
|
||||
cd ..
|
||||
cd ..
|
||||
FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz '/nn/7295866/20250127/nii/a_1.1_CyberKnife_head(MAR)_20250127111447_5.nii.gz' '/nn/7295866/20250127/nii/7_3D_SAG_T1_MPRAGE_+C_20250127132612_100.nii.gz' -g
|
||||
ls -ltr
|
||||
time FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz '/nn/7295866/20250127/nii/a_1.1_CyberKnife_head(MAR)_20250127111447_5.nii.gz' '/nn/7295866/20250127/nii/7_3D_SAG_T1_MPRAGE_+C_20250127132612_100.nii.gz' -g
|
||||
time FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz '/nn/7295866/20250127/nii/a_1.1_CyberKnife_head(MAR)_20250127111447_5.nii.gz' '/nn/7295866/20250127/nii/7_3D_SAG_T1_MPRAGE_+C_20250127132612_100.nii.gz' -g
|
||||
time FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz '/nn/7295866/20250127/nii/a_1.1_CyberKnife_head(MAR)_20250127111447_5.nii.gz' '/nn/7295866/20250127/nii/7_3D_SAG_T1_MPRAGE_+C_20250127132612_100.nii.gz' -g
|
||||
watch nvidia-smi
|
||||
cp oar3.py oar4.py
|
||||
watch nvidia-smi
|
||||
ls
|
||||
ls *gz
|
||||
cd onlylian/
|
||||
ls
|
||||
ls *gz
|
||||
cp '/nn/7295866/20250127/nii/a_1.1_CyberKnife_head(MAR)_20250127111447_5.nii.gz' ct.nii.gz
|
||||
cp '/nn/7295866/20250127/nii/7_3D_SAG_T1_MPRAGE_+C_20250127132612_100.nii.gz' t1c.nii.gz
|
||||
mri_synthmorph/mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz t1c.nii.gz ct.nii.gz -g
|
||||
time FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph mri_synthmorph/mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz t1c.nii.gz ct.nii.gz -g
|
||||
time FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz t1c.nii.gz ct.nii.gz -g
|
||||
time FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph -m affine -t trans.lta -o out-aff.nii.gz t1c.nii.gz ct.nii.gz -g
|
||||
python test2.py
|
||||
ls -ltr
|
||||
mv *.nii.gz 0/
|
||||
mkdir 0
|
||||
mv *.nii.gz 0/
|
||||
t ime FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph -m affine -t 0/trans.lta -o 0/out-aff.nii.gz 0/t1c.nii.gz 0/clipped.nii.gz -g
|
||||
rm trans.lta
|
||||
time FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph -m affine -t 0/trans.lta -o 0/out-aff.nii.gz 0/t1c.nii.gz 0/clipped.nii.gz -g
|
||||
time FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph o 0/out.nii.gz 0/t1c.nii.gz 0/clipped.nii.gz -g
|
||||
time FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph -o 0/out.nii.gz 0/t1c.nii.gz 0/clipped.nii.gz -g
|
||||
cd mri_synthmorph/models/
|
||||
wget https://surfer.nmr.mgh.harvard.edu/docs/synthmorph/synthmorph.deform.3.h5
|
||||
rm synthmorph.deform.3.h5
|
||||
cd ..
|
||||
cd ..
|
||||
time FREESURFER_HOME=/123/onlylian/mri_synthmorph mri_synthmorph/mri_synthmorph -m affine -t 0/trans.lta -o 0/out-aff.nii.gz 0/t1c.nii.gz 0/clipped.nii.gz -g
|
||||
grep oar3 ~/.bash_history
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
pip install blosc2
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
pip freeze
|
||||
pip freeze|grep acvl
|
||||
pip install acvl-utils==0.2
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
pip freeze|grep -i nnu
|
||||
pip install -U nnunetv2
|
||||
pip install nnunetv2==2.5.1
|
||||
pip install nnunetv2==2.4
|
||||
cd onlylian/
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
conda
|
||||
apt install libxrender1
|
||||
nvcc
|
||||
nvidia-smi
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
pip install tensorflow[and-cuda]
|
||||
python3 -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU'))"
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
ls mri_synthmorph/mri_synthmorph
|
||||
mri_synthmorph/mri_synthmorph
|
||||
mri_synthmorph/mri_synthmorph -h
|
||||
mri_synthmorph/mri_synthmorph register -h
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
python
|
||||
nvidia-smi
|
||||
cd onlylian/
|
||||
mri_synthmorph/mri_synthmorph register -h
|
||||
cd onlylian/
|
||||
python3 oar4.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
|
||||
pip freeze|grep torch
|
||||
|
|
|
|||
|
|
@ -1,98 +0,0 @@
|
|||
./2-infer.py /nn/7091925/20230208/CT/9 /nn/7091925/20230208/MR/7
|
||||
./1-move.py 6035638
|
||||
./2-infer.py /nn/6035638/20230209/CT/8 /nn/6035638/20230209/MR/7
|
||||
./1-move.py 7030265
|
||||
./2-infer.py /nn/7030265/20230209/CT/9 /nn/7030265/20230209/MR/7
|
||||
./1-move.py 6981439
|
||||
./2-infer.py /nn/6981439/20230210/CT/a /nn/6981439/20230210/MR/7
|
||||
./1-move.py 5665595
|
||||
./2-infer.py /nn/5665595/20230210/CT/9 /nn/5665595/20230210/MR/7
|
||||
./1-move.py 3903066
|
||||
./2-infer.py /nn/3903066/20230213/CT/a /nn/3903066/20230213/MR/7
|
||||
./1-move.py 3903066
|
||||
./2-infer.py /nn/3903066/20230213/CT/9 /nn/3903066/20230213/MR/7
|
||||
./1-move.py 5487071
|
||||
./2-infer.py /nn/5487071/20230213/CT/9 /nn/5487071/20230213/MR/7
|
||||
./1-move.py 6771041
|
||||
./2-infer.py /nn/6771041/20230214/CT/9 /nn/6771041/20230214/MR/7
|
||||
./1-move.py 5495897
|
||||
./2-infer.py /nn/5495897/20230214/CT/9 /nn/5495897/20230214/MR/7
|
||||
./1-move.py 6987123
|
||||
./2-infer.py /nn/6987123/20230215/CT/9 /nn/6987123/20230215/MR/7
|
||||
./1-move.py 3183636
|
||||
./2-infer.py /nn/3183636/20230215/CT/9 /nn/3183636/20230215/MR/7
|
||||
./1-move.py 5768342
|
||||
./2-infer.py /nn/5768342/20230216/CT/9 /nn/5768342/20230216/MR/7
|
||||
./1-move.py 5695691
|
||||
./2-infer.py /nn/5695691/20230216/CT/a /nn/5695691/20230216/MR/7
|
||||
./1-move.py 5768342
|
||||
./2-infer.py /nn/5768342/20230216/CT/9 /nn/5768342/20230216/MR/7
|
||||
./1-move.py 7123316
|
||||
./2-infer.py /nn/7123316/20230220/CT/9 /nn/7123316/20230220/MR/7
|
||||
./1-move.py 5831210
|
||||
./2-infer.py /nn/5831210/20230220/CT/c /nn/5831210/20230220/MR/a
|
||||
./1-move.py 3387187
|
||||
./2-infer.py /nn/3387187/20230221/CT/a /nn/3387187/20230221/MR/7
|
||||
./1-move.py 6803836
|
||||
./2-infer.py /nn/6803836/20230221/CT/10 /nn/6803836/20230221/MR/e
|
||||
./1-move.py
|
||||
./2-infer.py /nn/6466293/20230222/CT/a /nn/6466293/20230222/MR/7
|
||||
./1-move.py 2669302
|
||||
./2-infer.py /nn/2669302/20230223/CT/a /nn/2669302/20230223/MR/7
|
||||
./1-move.py 4607357
|
||||
./2-infer.py /nn/4607357/20230224/CT/a /nn/4607357/20230224/MR/7
|
||||
./1-move.py 7055212
|
||||
./2-infer.py /nn/7055212/20230224/CT/9 /nn/7055212/20230224/MR/7
|
||||
./1-move.py 5027429
|
||||
./2-infer.py /nn/5027429/20230306/CT/b /nn/5027429/20230306/MR/9
|
||||
./1-move.py 7123530
|
||||
./2-infer.py /nn/7123530/20230307/CT/a /nn/7123530/20230307/MR/7
|
||||
./1-move.py 7130932
|
||||
./2-infer.py /nn/7130932/20230307/CT/a /nn/7130932/20230307/MR/7
|
||||
./1-move.py 5771396
|
||||
./2-infer.py /nn/5771396/20230308/CT/a /nn/5771396/20230308/MR/7
|
||||
./1-move.py 7128131
|
||||
./2-infer.py /nn/7128131/20230310/CT/a /nn/7128131/20230310/MR/7
|
||||
./1-move.py 6412311
|
||||
./2-infer.py /nn/6412311/20230313/CT/9 /nn/6412311/20230313/MR/7
|
||||
./1-move.py
|
||||
./2-infer.py /nn/5494530/20230313/CT/a /nn/5494530/20230313/MR/7
|
||||
./1-move.py 7128706
|
||||
./2-infer.py /nn/7128706/20230310/CT/c /nn/7128706/20230310/MR
|
||||
./1-move.py 6925186
|
||||
./2-infer.py /nn/6925186/20230314/CT/a /nn/6925186/20230314/MR/7
|
||||
./1-move.py 3863530
|
||||
./1-move.py 3863530
|
||||
./2-infer.py /nn/3863530/20230314/CT/a /nn/3863530/20230314/MR/7
|
||||
./1-move.py 7131041
|
||||
./2-infer.py /nn/7131041/20230315/CT/a /nn/7131041/20230315/MR/7
|
||||
./1-move.py 5682089
|
||||
./2-infer.py /nn/5682089/20230315/CT/a /nn/5682089/20230315/MR/7
|
||||
./1-move.py 5553220
|
||||
./2-infer.py /nn/5553220/20230316/CT/a /nn/5553220/20230316/MR/7
|
||||
./1-move.py 3589548
|
||||
./2-infer.py /nn/3589548/20230317/CT/9 /nn/3589548/20230317/MR/7
|
||||
./1-move.py 2111161
|
||||
./2-infer.py /nn/2111161/20230317/CT/9 /nn/2111161/20230317/MR/7
|
||||
./1-move.py 6167673
|
||||
./2-infer.py /nn/6167673/20230320/CT/9 /nn/6167673/20230320/MR/7
|
||||
./1-move.py 2372501
|
||||
./2-infer.py /nn/2372501/20230320/CT/c /nn/2372501/20230320/MR/2
|
||||
./1-move.py 7134146
|
||||
./2-infer.py /nn/7134146/20230321/CT/a /nn/7134146/20230321/MR/7
|
||||
./1-move.py 6017134
|
||||
./2-infer.py /nn/6017134/20230321/CT/9 /nn/6017134/20230321/MR/7
|
||||
./1-move.py 5061967
|
||||
./2-infer.py /nn/5061967/20230322/CT/b /nn/5061967/20230322/MR/8
|
||||
./1-move.py 3060758
|
||||
./2-infer.py /nn/3060758/20230322/CT/a /nn/3060758/20230322/MR/7
|
||||
./1-move.py 6943475
|
||||
./2-infer.py /nn/6943475/20230323/CT/9 /nn/6943475/20230323/MR/7
|
||||
./1-move.py 5027838
|
||||
./2-infer.py /nn/5027838/20230323/CT/a /nn/5027838/20230323/MR/7
|
||||
./1-move.py 6783185
|
||||
./2-infer.py /nn/6783185/20230324/CT/a /nn/6783185/20230324/MR/7
|
||||
./1-move.py 4482158
|
||||
./2-infer.py /nn/4482158/20230324/CT/9 /nn/4482158/20230324/MR/7
|
||||
ls /nn
|
||||
ls -ltr /nn
|
||||
1
.conda/environments.txt
Executable file
1
.conda/environments.txt
Executable file
|
|
@ -0,0 +1 @@
|
|||
/opt/conda
|
||||
3
.gitconfig
Executable file
3
.gitconfig
Executable file
|
|
@ -0,0 +1,3 @@
|
|||
[user]
|
||||
email = xfr@dr.com
|
||||
name = xfr
|
||||
6
.gitignore
vendored
6
.gitignore
vendored
|
|
@ -160,8 +160,14 @@ cython_debug/
|
|||
#.idea/
|
||||
|
||||
.jupyter/
|
||||
.local/
|
||||
.npm/
|
||||
nnUNet_results/
|
||||
|
||||
*.nii
|
||||
*.nii.gz
|
||||
*.mat
|
||||
*.h5
|
||||
*.npz
|
||||
*.pth
|
||||
*log*.txt
|
||||
|
|
|
|||
0
.jupyter/jupyter_notebook_config.json
Normal file → Executable file
0
.jupyter/jupyter_notebook_config.json
Normal file → Executable file
0
.jupyter/lab/user-settings/@jupyterlab/docmanager-extension/plugin.jupyterlab-settings
Normal file → Executable file
0
.jupyter/lab/user-settings/@jupyterlab/docmanager-extension/plugin.jupyterlab-settings
Normal file → Executable file
2
.jupyter/lab/workspaces/lab-a511.jupyterlab-workspace
Normal file → Executable file
2
.jupyter/lab/workspaces/lab-a511.jupyterlab-workspace
Normal file → Executable file
|
|
@ -1 +1 @@
|
|||
{"data":{"layout-restorer:data":{"main":{"dock":{"type":"tab-area","currentIndex":1,"widgets":["editor:1-move.py","terminal:1","terminal:2","editor:2-infer.py","editor:adding.py"]},"mode":"multiple-document","current":"terminal:1"},"left":{"collapsed":false,"current":"filebrowser","widgets":["filebrowser","running-sessions","command-palette","jp-property-inspector","tab-manager","extensionmanager.main-view"]},"right":{"collapsed":true,"widgets":[]}},"@jupyterlab/settingeditor-extension:plugin":{"sizes":[0.16252955082742318,0.8374704491725768],"container":{"plugin":"@jupyterlab/terminal-extension:plugin","sizes":[0.4873891008009604,0.5126108991990396]}},"file-browser-filebrowser:cwd":{"path":""},"editor:2-infer.py":{"data":{"path":"2-infer.py","factory":"Editor"}},"editor:1-move.py":{"data":{"path":"1-move.py","factory":"Editor"}},"editor:adding.py":{"data":{"path":"adding.py","factory":"Editor"}},"terminal:1":{"data":{"name":"1"}},"terminal:2":{"data":{"name":"2"}}},"metadata":{"id":"/lab"}}
|
||||
{"data":{"layout-restorer:data":{"main":{"dock":{"type":"tab-area","currentIndex":0,"widgets":["editor:docker/v2/Dockerfile","terminal:1","editor:onlylian/oar4.py"]},"mode":"multiple-document","current":"editor:docker/v2/Dockerfile"},"left":{"collapsed":false,"current":"filebrowser","widgets":["filebrowser","running-sessions","command-palette","jp-property-inspector","tab-manager","extensionmanager.main-view"]},"right":{"collapsed":true,"widgets":[]}},"@jupyterlab/settingeditor-extension:plugin":{"sizes":[0.16252955082742318,0.8374704491725768],"container":{"plugin":"@jupyterlab/terminal-extension:plugin","sizes":[0.4873891008009604,0.5126108991990396]}},"file-browser-filebrowser:cwd":{"path":"onlylian"},"editor:onlylian/oar4.py":{"data":{"path":"onlylian/oar4.py","factory":"Editor"}},"editor:docker/v2/Dockerfile":{"data":{"path":"docker/v2/Dockerfile","factory":"Editor"}},"terminal:1":{"data":{"name":"1"}}},"metadata":{"id":"/lab"}}
|
||||
0
.jupyter/lab/workspaces/labworkspacesauto-c-4c4c.jupyterlab-workspace
Normal file → Executable file
0
.jupyter/lab/workspaces/labworkspacesauto-c-4c4c.jupyterlab-workspace
Normal file → Executable file
0
.jupyter/lab/workspaces/labworkspacesauto-d-fa4c.jupyterlab-workspace
Normal file → Executable file
0
.jupyter/lab/workspaces/labworkspacesauto-d-fa4c.jupyterlab-workspace
Normal file → Executable file
0
.jupyter/lab/workspaces/labworkspacesauto-m-cb31.jupyterlab-workspace
Normal file → Executable file
0
.jupyter/lab/workspaces/labworkspacesauto-m-cb31.jupyterlab-workspace
Normal file → Executable file
0
.jupyter/lab/workspaces/labworkspacesauto-q-6fd4.jupyterlab-workspace
Normal file → Executable file
0
.jupyter/lab/workspaces/labworkspacesauto-q-6fd4.jupyterlab-workspace
Normal file → Executable file
0
.jupyter/migrated
Normal file → Executable file
0
.jupyter/migrated
Normal file → Executable file
6
.keras/keras.json
Executable file
6
.keras/keras.json
Executable file
|
|
@ -0,0 +1,6 @@
|
|||
{
|
||||
"floatx": "float32",
|
||||
"epsilon": 1e-07,
|
||||
"backend": "tensorflow",
|
||||
"image_data_format": "channels_last"
|
||||
}
|
||||
8
.lesshst
Executable file
8
.lesshst
Executable file
|
|
@ -0,0 +1,8 @@
|
|||
.less-history-file:
|
||||
.search
|
||||
"nnu
|
||||
"torch
|
||||
"opencv
|
||||
.search
|
||||
"simpleitk
|
||||
"SimpleITK
|
||||
0
.local/share/Trash/info/Untitled Folder.trashinfo
Normal file → Executable file
0
.local/share/Trash/info/Untitled Folder.trashinfo
Normal file → Executable file
0
.local/share/Trash/info/resources 1.trashinfo
Normal file → Executable file
0
.local/share/Trash/info/resources 1.trashinfo
Normal file → Executable file
0
.local/share/Trash/info/resources.trashinfo
Normal file → Executable file
0
.local/share/Trash/info/resources.trashinfo
Normal file → Executable file
0
.local/share/Trash/info/untitled 1.txt.trashinfo
Normal file → Executable file
0
.local/share/Trash/info/untitled 1.txt.trashinfo
Normal file → Executable file
0
.local/share/Trash/info/untitled.txt.trashinfo
Normal file → Executable file
0
.local/share/Trash/info/untitled.txt.trashinfo
Normal file → Executable file
0
.local/share/jupyter/runtime/nbserver-1-open.html
Normal file → Executable file
0
.local/share/jupyter/runtime/nbserver-1-open.html
Normal file → Executable file
0
.local/share/jupyter/runtime/nbserver-1.json
Normal file → Executable file
0
.local/share/jupyter/runtime/nbserver-1.json
Normal file → Executable file
0
.local/share/jupyter/runtime/notebook_cookie_secret
Normal file → Executable file
0
.local/share/jupyter/runtime/notebook_cookie_secret
Normal file → Executable file
0
.npm/_cacache/index-v5/2b/cd/3ac6ae314de8839b74075c166d42a7bc667c6a0cdbbfe90261e360fda8bf
Normal file → Executable file
0
.npm/_cacache/index-v5/2b/cd/3ac6ae314de8839b74075c166d42a7bc667c6a0cdbbfe90261e360fda8bf
Normal file → Executable file
0
.npm/_cacache/index-v5/4c/64/23f8b5034fecc4dd91aeffce1682eea81041ebd44192c901522303dea70e
Normal file → Executable file
0
.npm/_cacache/index-v5/4c/64/23f8b5034fecc4dd91aeffce1682eea81041ebd44192c901522303dea70e
Normal file → Executable file
0
.npm/_cacache/index-v5/ac/d8/02b53e9340cf22cc0e589680dc8ed1731bb9c0adda97021357182d36095a
Normal file → Executable file
0
.npm/_cacache/index-v5/ac/d8/02b53e9340cf22cc0e589680dc8ed1731bb9c0adda97021357182d36095a
Normal file → Executable file
0
.npm/_cacache/index-v5/e6/c0/741f8c19375dcfef585384ba651efe7f725e7379ed9fc932281f5a97d9af
Normal file → Executable file
0
.npm/_cacache/index-v5/e6/c0/741f8c19375dcfef585384ba651efe7f725e7379ed9fc932281f5a97d9af
Normal file → Executable file
24
.python_history
Normal file → Executable file
24
.python_history
Normal file → Executable file
|
|
@ -18,3 +18,27 @@ monai._version()
|
|||
monai._version
|
||||
print(monai._version)
|
||||
monai.__version__
|
||||
import torch
|
||||
torch.cuda.is_available()
|
||||
import torch
|
||||
torch.cuda.is_available()
|
||||
nvidia-smi
|
||||
import torch
|
||||
torch.cuda.is_available()
|
||||
import torch
|
||||
torch.cuda.is_available()
|
||||
torch.cuda.device_count()
|
||||
torch.cuda.current_device()
|
||||
torch.cuda.get_device_name(0)
|
||||
import pyradise.fileio as ps_io
|
||||
conv_conf = ps_io.RTSSConverter3DConfiguration()
|
||||
conv_conf = ps_io.RTSSConverter3DConfiguration()
|
||||
type(conv_conf)
|
||||
conv_conf.__class__
|
||||
conv_conf.__class__..__name__
|
||||
conv_conf.__class__.__name__
|
||||
type(conv_conf).__name__
|
||||
str(type(conv_conf))
|
||||
type(conv_conf).__name__
|
||||
from tensorflow.python.client import device_lib
|
||||
print(device_lib.list_local_devices())
|
||||
|
|
|
|||
1
.ssh/known_hosts
Executable file
1
.ssh/known_hosts
Executable file
|
|
@ -0,0 +1 @@
|
|||
|1|4vxGI0/l98zY1f4TsRsmEXtNqOA=|FLviQM2mLzejJt7p1mGN+cUuVG4= ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIBKVS2CCO86WZc9A4GtDx4PIz1Tq91/a2FS8HmgjM/EW
|
||||
3
.wget-hsts
Normal file → Executable file
3
.wget-hsts
Normal file → Executable file
|
|
@ -2,4 +2,5 @@
|
|||
# Edit at your own risk.
|
||||
# <hostname> <port> <incl. subdomains> <created> <max-age>
|
||||
raw.githubusercontent.com 0 0 1691530822 31536000
|
||||
github.com 0 1 1691530822 31536000
|
||||
surfer.nmr.mgh.harvard.edu 0 1 1738329857 31536000
|
||||
github.com 0 1 1731403394 31536000
|
||||
|
|
|
|||
BIN
0/dcm2niix
Executable file
BIN
0/dcm2niix
Executable file
Binary file not shown.
BIN
0/dcm2niix_lnx.zip
Executable file
BIN
0/dcm2niix_lnx.zip
Executable file
Binary file not shown.
BIN
0/mri_synthmorph.zip
Executable file
BIN
0/mri_synthmorph.zip
Executable file
Binary file not shown.
53
3-rtss.py
Executable file
53
3-rtss.py
Executable file
|
|
@ -0,0 +1,53 @@
|
|||
|
||||
import SimpleITK as sitk
|
||||
from rt_utils import RTStructBuilder
|
||||
|
||||
import numpy as np
|
||||
|
||||
DCM_CT = '/nn/3378417/20241112/CT/8'
|
||||
NII_CT = "/nn/3378417/20241112/nii/8_1.1_CyberKnife_head(MAR)_20241112110016_4.nii.gz"
|
||||
label_file = "/nn/3378417/20241112/nii/8_1.1_CyberKnife_head(MAR)_20241112110016.label.nii.gz"
|
||||
rtss_file = '/nn/3378417/20241112/CT/8-rtss.dcm'
|
||||
|
||||
# reg_transform(NII_CT, NII_MR, output_file, label_file)
|
||||
|
||||
reader = sitk.ImageSeriesReader()
|
||||
dicom_names = reader.GetGDCMSeriesFileNames(DCM_CT)
|
||||
reader.SetFileNames(dicom_names)
|
||||
# reader.SetFileNames(sorted(dicom_names))
|
||||
reader.MetaDataDictionaryArrayUpdateOn()
|
||||
reader.LoadPrivateTagsOn()
|
||||
image = reader.Execute()
|
||||
sitk.WriteImage(image, '0/image.nii.gz')
|
||||
|
||||
nnU = sitk.ReadImage(label_file)
|
||||
nnU = sitk.Resample(nnU, image, sitk.Transform(), sitk.sitkNearestNeighbor)
|
||||
|
||||
sitk.WriteImage(nnU, '0/nnU.nii.gz')
|
||||
|
||||
ccfilter = sitk.ConnectedComponentImageFilter ()
|
||||
nnUCC = ccfilter.Execute(nnU)
|
||||
ObjectCount1 = ccfilter.GetObjectCount()
|
||||
|
||||
rtstruct = RTStructBuilder.create_new(dicom_series_path=DCM_CT)
|
||||
|
||||
print(ObjectCount1)
|
||||
for j1 in range(ObjectCount1):
|
||||
label1 = sitk.BinaryThreshold(nnUCC, j1+1, j1+1)
|
||||
# label1 = sitk.AntiAliasBinary(label1)
|
||||
|
||||
mask = sitk.GetArrayFromImage(label1).astype(bool)
|
||||
mask = np.transpose(mask, (1, 2, 0))
|
||||
# continue
|
||||
if mask.any():
|
||||
print(j1)
|
||||
rtstruct.add_roi(
|
||||
mask=mask,
|
||||
# use_pin_hole=True,
|
||||
# name="n%d"%n,
|
||||
)
|
||||
|
||||
print(rtss_file)
|
||||
rtstruct.save(rtss_file)
|
||||
|
||||
# return rtss_file
|
||||
BIN
6jj_lths.mat
BIN
6jj_lths.mat
Binary file not shown.
|
|
@ -0,0 +1,69 @@
|
|||
{
|
||||
"Modality": "MR",
|
||||
"MagneticFieldStrength": 1.5,
|
||||
"ImagingFrequency": 63.6788,
|
||||
"Manufacturer": "Siemens",
|
||||
"ManufacturersModelName": "Aera",
|
||||
"InstitutionName": "NTUH",
|
||||
"InstitutionalDepartmentName": "Department",
|
||||
"InstitutionAddress": "Zhongshan_S._Rd._7_Taipei_Zhongzheng_TW_10002",
|
||||
"DeviceSerialNumber": "141566",
|
||||
"StationName": "ESIMR01MC01",
|
||||
"BodyPartExamined": "BRAIN",
|
||||
"PatientPosition": "HFS",
|
||||
"ProcedureStepDescription": "cyberknife_head",
|
||||
"SoftwareVersions": "syngo_MR_E11",
|
||||
"MRAcquisitionType": "3D",
|
||||
"SeriesDescription": "3D_SAG_T1_MPRAGE_+C_MPR_Tra",
|
||||
"ProtocolName": "3D_SAG_T1_MPRAGE_+C_MPR_Tra",
|
||||
"ScanningSequence": "GR_IR",
|
||||
"SequenceVariant": "SK_SP_MP_OSP",
|
||||
"ScanOptions": "IR",
|
||||
"SequenceName": "_tfl3d1rs16ns",
|
||||
"ImageType": ["DERIVED", "PRIMARY", "MPR", "NORM", "DIS2D", "SH5", "1", "FIL"],
|
||||
"RawImage": false,
|
||||
"SeriesNumber": 13,
|
||||
"AcquisitionTime": "14:26:11.657500",
|
||||
"AcquisitionNumber": 1,
|
||||
"SliceThickness": 1,
|
||||
"SAR": 0.0200454,
|
||||
"EchoTime": 0.00461,
|
||||
"RepetitionTime": 2,
|
||||
"InversionTime": 0.797,
|
||||
"FlipAngle": 12,
|
||||
"PartialFourier": 1,
|
||||
"BaseResolution": 256,
|
||||
"ShimSetting": [
|
||||
-3760,
|
||||
8852,
|
||||
-7021,
|
||||
-2213,
|
||||
-115,
|
||||
-114,
|
||||
-133,
|
||||
19 ],
|
||||
"TxRefAmp": 319.32,
|
||||
"PhaseResolution": 1,
|
||||
"PhaseOversampling": 0.09,
|
||||
"ReceiveCoilName": "HeadNeck_20",
|
||||
"ReceiveCoilActiveElements": "HE1-4;NE1,2",
|
||||
"CoilString": "HE1-4;NE1_2",
|
||||
"PulseSequenceDetails": "%SiemensSeq%_tfl",
|
||||
"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
|
||||
"PercentPhaseFOV": 100,
|
||||
"PhaseEncodingSteps": 279,
|
||||
"AcquisitionMatrixPE": 256,
|
||||
"ReconMatrixPE": 220,
|
||||
"PixelBandwidth": 130,
|
||||
"DwellTime": 1.5e-05,
|
||||
"ImageOrientationPatientDICOM": [
|
||||
1,
|
||||
0,
|
||||
0,
|
||||
0,
|
||||
1,
|
||||
0 ],
|
||||
"InPlanePhaseEncodingDirectionDICOM": "COL",
|
||||
"ConversionSoftware": "dcm2niix",
|
||||
"ConversionSoftwareVersion": "v1.0.20181125 (JP2:OpenJPEG) GCC9.3.0"
|
||||
}
|
||||
29
P:/nn/3894670/20241111/nii/a_C+_20241111153649_5.json
Executable file
29
P:/nn/3894670/20241111/nii/a_C+_20241111153649_5.json
Executable file
|
|
@ -0,0 +1,29 @@
|
|||
{
|
||||
"Modality": "CT",
|
||||
"Manufacturer": "GE",
|
||||
"ManufacturersModelName": "Discovery_RT",
|
||||
"InstitutionName": "NTUH",
|
||||
"InstitutionAddress": "123",
|
||||
"StationName": "GERTCT",
|
||||
"PatientPosition": "HFS",
|
||||
"ProcedureStepDescription": "3894670",
|
||||
"SoftwareVersions": "rt_bjcl.83",
|
||||
"SeriesDescription": "C+",
|
||||
"ProtocolName": "C+",
|
||||
"ScanOptions": "HELICAL_MODE",
|
||||
"ImageType": ["ORIGINAL", "PRIMARY", "AXIAL"],
|
||||
"SeriesNumber": 5,
|
||||
"AcquisitionTime": "15:44:55.235500",
|
||||
"AcquisitionNumber": 1,
|
||||
"XRayExposure": 53,
|
||||
"ReconMatrixPE": 512,
|
||||
"ImageOrientationPatientDICOM": [
|
||||
1,
|
||||
0,
|
||||
0,
|
||||
0,
|
||||
1,
|
||||
0 ],
|
||||
"ConversionSoftware": "dcm2niix",
|
||||
"ConversionSoftwareVersion": "v1.0.20181125 (JP2:OpenJPEG) GCC9.3.0"
|
||||
}
|
||||
0
adding.py
Normal file → Executable file
0
adding.py
Normal file → Executable file
BIN
bcngawwk.mat
BIN
bcngawwk.mat
Binary file not shown.
63
docker/v1.5/Dockerfile
Executable file
63
docker/v1.5/Dockerfile
Executable file
|
|
@ -0,0 +1,63 @@
|
|||
# FROM nvcr.io/nvidia/clara-train-sdk:v4.1
|
||||
FROM nvcr.io/nvidia/pytorch:22.08-py3
|
||||
|
||||
|
||||
# apt
|
||||
RUN apt-get update -y \
|
||||
&& apt-get install libxrender1 openssh-server pigz sudo -y
|
||||
|
||||
#conda
|
||||
# RUN conda update -y -n base conda
|
||||
# RUN conda install -y -n base conda-libmamba-solver
|
||||
# RUN conda config -y --set solver libmamba
|
||||
|
||||
# pip
|
||||
# RUN pip install --upgrade pip
|
||||
|
||||
# RUN pip install antspyx itk-elastix nipype nnunet rt_utils
|
||||
RUN pip install antspyx nipype nnunet nnunetv2 simpleitk==2.3.1 tensorflow # too large .... install first
|
||||
# RUN pip install itk-elastix==0.13.0
|
||||
# RUN pip install itk-elastix
|
||||
# RUN pip install --upgrade git+https://github.com/FabianIsensee/hiddenlayer.git@more_plotted_details#egg=hiddenlayer
|
||||
|
||||
# RUN pip install --upgrade git+https://github.com/FabianIsensee/hiddenlayer.git
|
||||
# RUN pip install --upgrade git+https://github.com/rohitrango/fireants.git
|
||||
# RUN pip install git+https://github.com/qurit/rt-utils.git@5bab9ffcc8fe19dd775e940afdc3d8f48f869150 # fix FrameOfReferenceUID
|
||||
|
||||
# RUN pip install git+https://github.com/adalca/neurite.git git+https://github.com/freesurfer/surfa.git git+https://github.com/voxelmorph/voxelmorph.git
|
||||
|
||||
# WORKDIR /workspace
|
||||
WORKDIR /123
|
||||
COPY requirements.txt /123
|
||||
RUN pip install -r requirements.txt
|
||||
|
||||
RUN wget https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20240202/dcm2niix_lnx.zip
|
||||
RUN unzip dcm2niix_lnx.zip
|
||||
RUN cp dcm2niix /usr/bin
|
||||
|
||||
# nnUNet
|
||||
|
||||
ENV nnUNet_raw_data_base="/workspace/nnUNet_raw_data_base"
|
||||
ENV nnUNet_preprocessed="/workspace/nnUNet_preprocessed"
|
||||
ENV RESULTS_FOLDER="/workspace/nnUNet_trained_models"
|
||||
|
||||
ENV nnUNet_raw="/workspace/v2/nnUNet_raw"
|
||||
ENV nnUNet_preprocessed="/workspace/v2/nnUNet_preprocessed"
|
||||
ENV nnUNet_results="/workspace/v2/nnUNet_results"
|
||||
|
||||
# SSH server
|
||||
#RUN echo 'root:password' | chpasswd
|
||||
#RUN echo "PasswordAuthentication yes" >> /etc/ssh/sshd_config
|
||||
#RUN echo "PermitRootLogin yes" >> /etc/ssh/sshd_config
|
||||
#ENTRYPOINT service ssh restart && env >> /etc/environment && bash
|
||||
#EXPOSE 22
|
||||
|
||||
# Masonite
|
||||
EXPOSE 8000
|
||||
|
||||
# jupyter
|
||||
ENTRYPOINT jupyter-lab
|
||||
EXPOSE 8888
|
||||
|
||||
# pynetdicom
|
||||
EXPOSE 11120
|
||||
2
docker/v1.5/build.sh
Executable file
2
docker/v1.5/build.sh
Executable file
|
|
@ -0,0 +1,2 @@
|
|||
# DOCKER_BUILDKIT=1 docker build -t 123:v2 .
|
||||
docker build -t 123:v2 .
|
||||
30
docker/v1.5/qrun.sh
Executable file
30
docker/v1.5/qrun.sh
Executable file
|
|
@ -0,0 +1,30 @@
|
|||
|
||||
docker stop 123
|
||||
docker rm 123
|
||||
|
||||
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
|
||||
#DIR="$(dirname $( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd ))"
|
||||
|
||||
export dockerImage=123:v2
|
||||
|
||||
#docker run --gpus all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 -it --rm -v $DIR:/workspace $dockerImage /bin/bash
|
||||
# GPU=nvidia0 gpu-docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 -it --rm \
|
||||
#GPU=nvidia0 gpu-docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \
|
||||
|
||||
|
||||
|
||||
docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \
|
||||
--name 123 \
|
||||
--volume=/share/CACHEDEV1_DATA/.qpkg/NVIDIA_GPU_DRV/usr:/usr/local/nvidia \
|
||||
--device /dev/nvidiactl:/dev/nvidiactl --device /dev/nvidia-uvm:/dev/nvidia-uvm --device /dev/nvidia0:/dev/nvidia0 \
|
||||
-v /share/WORKSPACE/nnUNet:/workspace \
|
||||
-v /share/Public/git/123:/123 \
|
||||
-v /share/Public/git/123:/root \
|
||||
-v /share/Public/nn:/nn \
|
||||
-v /share/Public/Patient:/Patient \
|
||||
-p 8000:8000 \
|
||||
-p 8888:8888 \
|
||||
-p 11120:11120 \
|
||||
--restart=always \
|
||||
$dockerImage &
|
||||
|
||||
16
docker/v1.5/requirements.txt
Executable file
16
docker/v1.5/requirements.txt
Executable file
|
|
@ -0,0 +1,16 @@
|
|||
masonite>=4.0,<5.0
|
||||
masonite-orm>=2.0,<3.0
|
||||
|
||||
opencv-python<4.6 # for rt-utils
|
||||
|
||||
# fireants
|
||||
itk-elastix
|
||||
pynetdicom
|
||||
pyradise
|
||||
rt-utils
|
||||
|
||||
git+https://github.com/FabianIsensee/hiddenlayer.git
|
||||
|
||||
git+https://github.com/adalca/neurite.git
|
||||
git+https://github.com/freesurfer/surfa.git
|
||||
git+https://github.com/voxelmorph/voxelmorph.git
|
||||
|
|
@ -2,7 +2,7 @@ FROM nvcr.io/nvidia/clara-train-sdk:v4.1
|
|||
|
||||
# apt
|
||||
RUN apt-get update -y \
|
||||
&& apt-get install dcm2niix openssh-server pigz sudo -y
|
||||
&& apt-get install openssh-server pigz sudo -y
|
||||
|
||||
# pip
|
||||
# RUN pip install antspyx itk-elastix nipype nnunet rt_utils
|
||||
|
|
@ -17,6 +17,10 @@ WORKDIR /123
|
|||
COPY requirements.txt /123
|
||||
RUN pip install -r requirements.txt
|
||||
|
||||
RUN wget https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20240202/dcm2niix_lnx.zip
|
||||
RUN unzip dcm2niix_lnx.zip
|
||||
RUN cp dcm2niix /usr/bin
|
||||
|
||||
# nnUNet
|
||||
|
||||
ENV nnUNet_raw_data_base="/workspace/nnUNet_raw_data_base"
|
||||
|
|
@ -1,3 +1,7 @@
|
|||
|
||||
docker stop 123
|
||||
docker rm 123
|
||||
|
||||
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
|
||||
#DIR="$(dirname $( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd ))"
|
||||
|
||||
|
|
@ -6,8 +10,13 @@ export dockerImage=123:v0
|
|||
#docker run --gpus all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 -it --rm -v $DIR:/workspace $dockerImage /bin/bash
|
||||
# GPU=nvidia0 gpu-docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 -it --rm \
|
||||
#GPU=nvidia0 gpu-docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \
|
||||
|
||||
|
||||
|
||||
docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \
|
||||
--name 123 \
|
||||
--volume=/share/CACHEDEV1_DATA/.qpkg/NVIDIA_GPU_DRV/usr:/usr/local/nvidia \
|
||||
--device /dev/nvidiactl:/dev/nvidiactl --device /dev/nvidia-uvm:/dev/nvidia-uvm --device /dev/nvidia0:/dev/nvidia0 \
|
||||
-v /share/WORKSPACE/nnUNet:/workspace \
|
||||
-v /share/Public/git/123:/123 \
|
||||
-v /share/Public/git/123:/root \
|
||||
|
|
@ -16,8 +25,6 @@ docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \
|
|||
-p 8000:8000 \
|
||||
-p 8888:8888 \
|
||||
-p 11120:11120 \
|
||||
--restart=always \
|
||||
$dockerImage &
|
||||
|
||||
|
||||
# Then recreate, adding GPU in runtime
|
||||
|
||||
0
docker/requirements.txt → docker/v1/requirements.txt
Normal file → Executable file
0
docker/requirements.txt → docker/v1/requirements.txt
Normal file → Executable file
51
docker/v2/Dockerfile
Executable file
51
docker/v2/Dockerfile
Executable file
|
|
@ -0,0 +1,51 @@
|
|||
# FROM nvcr.io/nvidia/clara-train-sdk:v4.1
|
||||
# FROM nvcr.io/nvidia/pytorch:22.08-py3
|
||||
# FROM nvcr.io/nvidia/pytorch:24.01-py3
|
||||
FROM nvcr.io/nvidia/tensorflow:24.03-tf2-py3
|
||||
|
||||
# apt
|
||||
RUN apt-get update -y \
|
||||
&& apt-get install libxrender1 openssh-server pigz sudo -y
|
||||
|
||||
# pip
|
||||
|
||||
# RUN pip install antspyx itk-elastix nipype nnunet nnunetv2 simpleitk==2.3.1 tensorflow[and-cuda] #too large .... install first
|
||||
|
||||
RUN pip install "torch<2.6" torchvision torchaudio --index-url https://download.pytorch.org/whl/cu124
|
||||
RUN pip install antspyx itk-elastix nipype nnunet nnunetv2 simpleitk==2.3.1 #too large .... install first
|
||||
|
||||
# WORKDIR /workspace
|
||||
WORKDIR /123
|
||||
COPY requirements.txt /123
|
||||
RUN pip install -r requirements.txt
|
||||
|
||||
RUN wget https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20240202/dcm2niix_lnx.zip
|
||||
RUN unzip dcm2niix_lnx.zip
|
||||
RUN cp dcm2niix /usr/bin
|
||||
|
||||
# nnUNet
|
||||
|
||||
ENV nnUNet_raw_data_base="/workspace/nnUNet_raw_data_base"
|
||||
ENV nnUNet_preprocessed="/workspace/nnUNet_preprocessed"
|
||||
ENV RESULTS_FOLDER="/workspace/nnUNet_trained_models"
|
||||
|
||||
ENV nnUNet_raw="/workspace/v2/nnUNet_raw"
|
||||
ENV nnUNet_preprocessed="/workspace/v2/nnUNet_preprocessed"
|
||||
ENV nnUNet_results="/workspace/v2/nnUNet_results"
|
||||
|
||||
# SSH server
|
||||
#RUN echo 'root:password' | chpasswd
|
||||
#RUN echo "PasswordAuthentication yes" >> /etc/ssh/sshd_config
|
||||
#RUN echo "PermitRootLogin yes" >> /etc/ssh/sshd_config
|
||||
#ENTRYPOINT service ssh restart && env >> /etc/environment && bash
|
||||
#EXPOSE 22
|
||||
|
||||
# Masonite
|
||||
EXPOSE 8000
|
||||
|
||||
# jupyter
|
||||
ENTRYPOINT jupyter-lab
|
||||
EXPOSE 8888
|
||||
|
||||
# pynetdicom
|
||||
EXPOSE 11120
|
||||
2
docker/v2/build.sh
Executable file
2
docker/v2/build.sh
Executable file
|
|
@ -0,0 +1,2 @@
|
|||
# DOCKER_BUILDKIT=1 docker build -t 123:v2 .
|
||||
docker build -t 123:v2 .
|
||||
30
docker/v2/qrun.sh
Executable file
30
docker/v2/qrun.sh
Executable file
|
|
@ -0,0 +1,30 @@
|
|||
|
||||
docker stop 123
|
||||
docker rm 123
|
||||
|
||||
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
|
||||
#DIR="$(dirname $( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd ))"
|
||||
|
||||
export dockerImage=123:v2
|
||||
|
||||
#docker run --gpus all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 -it --rm -v $DIR:/workspace $dockerImage /bin/bash
|
||||
# GPU=nvidia0 gpu-docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 -it --rm \
|
||||
#GPU=nvidia0 gpu-docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \
|
||||
|
||||
|
||||
|
||||
docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \
|
||||
--name 123 \
|
||||
--volume=/share/CACHEDEV1_DATA/.qpkg/NVIDIA_GPU_DRV/usr:/usr/local/nvidia \
|
||||
--device /dev/nvidiactl:/dev/nvidiactl --device /dev/nvidia-uvm:/dev/nvidia-uvm --device /dev/nvidia0:/dev/nvidia0 \
|
||||
-v /share/WORKSPACE/nnUNet:/workspace \
|
||||
-v /share/Public/git/123:/123 \
|
||||
-v /share/Public/git/123:/root \
|
||||
-v /share/Public/nn:/nn \
|
||||
-v /share/Public/Patient:/Patient \
|
||||
-p 8000:8000 \
|
||||
-p 8888:8888 \
|
||||
-p 11120:11120 \
|
||||
--restart=always \
|
||||
$dockerImage &
|
||||
|
||||
14
docker/v2/requirements.txt
Executable file
14
docker/v2/requirements.txt
Executable file
|
|
@ -0,0 +1,14 @@
|
|||
#masonite>=4.0,<5.0
|
||||
#masonite-orm>=2.0,<3.0
|
||||
|
||||
opencv-python<4.6 # for rt-utils
|
||||
|
||||
pynetdicom
|
||||
pyradise
|
||||
rt-utils
|
||||
|
||||
git+https://github.com/FabianIsensee/hiddenlayer.git
|
||||
|
||||
git+https://github.com/adalca/neurite.git
|
||||
git+https://github.com/freesurfer/surfa.git
|
||||
git+https://github.com/voxelmorph/voxelmorph.git
|
||||
1
fireants
Submodule
1
fireants
Submodule
|
|
@ -0,0 +1 @@
|
|||
Subproject commit d363d8240835f968e872e462b83ea461a1d57f4b
|
||||
0
myapp/.env-example
Normal file → Executable file
0
myapp/.env-example
Normal file → Executable file
0
myapp/.env.testing
Normal file → Executable file
0
myapp/.env.testing
Normal file → Executable file
0
myapp/.gitignore
vendored
Normal file → Executable file
0
myapp/.gitignore
vendored
Normal file → Executable file
0
myapp/Kernel.py
Normal file → Executable file
0
myapp/Kernel.py
Normal file → Executable file
0
myapp/app/__init__.py
Normal file → Executable file
0
myapp/app/__init__.py
Normal file → Executable file
0
myapp/app/controllers/BlogController.py
Normal file → Executable file
0
myapp/app/controllers/BlogController.py
Normal file → Executable file
0
myapp/app/controllers/PatientController.py
Normal file → Executable file
0
myapp/app/controllers/PatientController.py
Normal file → Executable file
0
myapp/app/controllers/WelcomeController.py
Normal file → Executable file
0
myapp/app/controllers/WelcomeController.py
Normal file → Executable file
0
myapp/app/controllers/__init__.py
Normal file → Executable file
0
myapp/app/controllers/__init__.py
Normal file → Executable file
0
myapp/app/controllers/api/UsersController.py
Normal file → Executable file
0
myapp/app/controllers/api/UsersController.py
Normal file → Executable file
0
myapp/app/middlewares/AuthenticationMiddleware.py
Normal file → Executable file
0
myapp/app/middlewares/AuthenticationMiddleware.py
Normal file → Executable file
0
myapp/app/middlewares/VerifyCsrfToken.py
Normal file → Executable file
0
myapp/app/middlewares/VerifyCsrfToken.py
Normal file → Executable file
0
myapp/app/middlewares/__init__.py
Normal file → Executable file
0
myapp/app/middlewares/__init__.py
Normal file → Executable file
0
myapp/app/models/User.py
Normal file → Executable file
0
myapp/app/models/User.py
Normal file → Executable file
0
myapp/app/providers/AppProvider.py
Normal file → Executable file
0
myapp/app/providers/AppProvider.py
Normal file → Executable file
0
myapp/app/providers/__init__.py
Normal file → Executable file
0
myapp/app/providers/__init__.py
Normal file → Executable file
0
myapp/config/__init__.py
Normal file → Executable file
0
myapp/config/__init__.py
Normal file → Executable file
0
myapp/config/api.py
Normal file → Executable file
0
myapp/config/api.py
Normal file → Executable file
0
myapp/config/application.py
Normal file → Executable file
0
myapp/config/application.py
Normal file → Executable file
0
myapp/config/auth.py
Normal file → Executable file
0
myapp/config/auth.py
Normal file → Executable file
0
myapp/config/broadcast.py
Normal file → Executable file
0
myapp/config/broadcast.py
Normal file → Executable file
0
myapp/config/cache.py
Normal file → Executable file
0
myapp/config/cache.py
Normal file → Executable file
0
myapp/config/database.py
Normal file → Executable file
0
myapp/config/database.py
Normal file → Executable file
0
myapp/config/exceptions.py
Normal file → Executable file
0
myapp/config/exceptions.py
Normal file → Executable file
0
myapp/config/filesystem.py
Normal file → Executable file
0
myapp/config/filesystem.py
Normal file → Executable file
0
myapp/config/mail.py
Normal file → Executable file
0
myapp/config/mail.py
Normal file → Executable file
0
myapp/config/notification.py
Normal file → Executable file
0
myapp/config/notification.py
Normal file → Executable file
0
myapp/config/providers.py
Normal file → Executable file
0
myapp/config/providers.py
Normal file → Executable file
0
myapp/config/queue.py
Normal file → Executable file
0
myapp/config/queue.py
Normal file → Executable file
0
myapp/config/session.py
Normal file → Executable file
0
myapp/config/session.py
Normal file → Executable file
0
myapp/craft
Normal file → Executable file
0
myapp/craft
Normal file → Executable file
0
myapp/databases/migrations/2021_01_09_033202_create_password_reset_table.py
Normal file → Executable file
0
myapp/databases/migrations/2021_01_09_033202_create_password_reset_table.py
Normal file → Executable file
0
myapp/databases/migrations/2021_01_09_043202_create_users_table.py
Normal file → Executable file
0
myapp/databases/migrations/2021_01_09_043202_create_users_table.py
Normal file → Executable file
0
myapp/databases/seeds/__init__.py
Normal file → Executable file
0
myapp/databases/seeds/__init__.py
Normal file → Executable file
0
myapp/databases/seeds/database_seeder.py
Normal file → Executable file
0
myapp/databases/seeds/database_seeder.py
Normal file → Executable file
0
myapp/databases/seeds/user_table_seeder.py
Normal file → Executable file
0
myapp/databases/seeds/user_table_seeder.py
Normal file → Executable file
0
myapp/makefile
Normal file → Executable file
0
myapp/makefile
Normal file → Executable file
0
myapp/package.json
Normal file → Executable file
0
myapp/package.json
Normal file → Executable file
0
myapp/pyproject.toml
Normal file → Executable file
0
myapp/pyproject.toml
Normal file → Executable file
0
myapp/requirements.txt
Normal file → Executable file
0
myapp/requirements.txt
Normal file → Executable file
0
myapp/resources/css/app.css
Normal file → Executable file
0
myapp/resources/css/app.css
Normal file → Executable file
0
myapp/resources/js/app.js
Normal file → Executable file
0
myapp/resources/js/app.js
Normal file → Executable file
0
myapp/resources/js/bootstrap.js
vendored
Normal file → Executable file
0
myapp/resources/js/bootstrap.js
vendored
Normal file → Executable file
0
myapp/routes/api.py
Normal file → Executable file
0
myapp/routes/api.py
Normal file → Executable file
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Reference in a new issue