500 lines
20 KiB
Bash
Executable file
500 lines
20 KiB
Bash
Executable file
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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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/1561614/20241220/CT/a /nn/1561614/20241220/MR/8
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./1-move.py 2641998
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./2-infer.py /nn/2641998/20241220/CT/c /nn/2641998/20241220/MR/3
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./1-move.py 5108920
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./1-move.py 5435462
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./1-move.py 2944822
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./1-move.py 7287366
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./1-move.py 6405610
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./1-move.py 7286032
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./1-move.py 1786330
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./1-move.py 7284108
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./1-move.py 7365592
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./1-move.py 4365592
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./1-move.py 6901803
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./2-infer.py /nn/6901803/20241230/CT/9 /nn/6901803/20241230/MR/8
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./1-move.py 7146030
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./2-infer.py /nn/7146030/20241230/CT/b /nn/7146030/20241230/MR/8
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./1-move.py 3560986
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./2-infer.py /nn/3560986/20241231/CT/9 /nn/3560986/20241231/MR/8
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./1-move.py 6075924
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./2-infer.py /nn/6075924/20241231/CT/a /nn/6075924/20241231/MR/8
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./1-move.py 2367245
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./2-infer.py /nn/2367245/20241223/CT/b /nn/2367245/20241231/MR/7
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./1-move.py 2367245
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./1-move.py 3018505
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./1-move.py 6827885
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./1-move.py 2556090
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./1-move.py 6902522
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./1-move.py 5908183
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./1-move.py 7165972
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./1-move.py 5835974
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./2-infer.py /nn/5835974/20250107/CT/9 /nn/5835974/20250107/MR/7
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./1-move.py 7239182
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./1-move.py 7239182
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./2-infer.py /nn/7239182/20250107/CT/8 /nn/7239182/20250107/MR/7
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./1-move.py 6248872
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./2-infer.py /nn/6248872/20250108/CT/a /nn/6248872/20250108/MR/8
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./1-move.py 7223127
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./1-move.py 1918501
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./2-infer.py /nn/1918501/20250109/CT/a /nn/1918501/20250109/MR/8
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./1-move.py 8049454
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./2-infer.py /nn/8049454/20250109/CT/9 /nn/8049454/20250109/MR/8
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./1-move.py A105575
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./1-move.py 6217784
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./2-infer.py /nn/6217784/20250110/CT/2 /nn/A105575/20250107/MR/8
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./1-move.py 6736489
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./2-infer.py /nn/6736489/20250110/CT/a /nn/6736489/20250110/MR/8
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./1-move.py 6052644
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./2-infer.py /nn/6052644/20250110/CT/b /nn/6052644/20250110/MR/9
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./1-move.py 6052644
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./2-infer.py /nn/6052644/20250110/CT/b /nn/6052644/20250110/MR/9
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./1-move.py 2516940
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./2-infer.py /nn/2516940/20250113/CT/a /nn/2516940/20250113/MR/7
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./1-move.py 7190177
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./2-infer.py /nn/7190177/20250113/CT/b /nn/7190177/20250113/MR/8
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./1-move.py 4398001
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./1-move.py 4003636
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./1-move.py 7233916
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./2-infer.py /nn/7233916/20250115/CT/b /nn/7233916/20250115/MR/7
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./1-move.py 7295438
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./2-infer.py /nn/7295438/20250115/CT/d /nn/7295438/20250115/MR/9
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./1-move.py 5337151
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./1-move.py 5337151
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./1-move.py 5337151
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./1-move.py 5131302
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./1-move.py 5337151
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./1-move.py 7283904
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./1-move.py 4182983
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./2-infer.py /nn/4182983/20250117/CT/a /nn/4182983/20250117/MR/6
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./1-move.py 5517865
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./1-move.py 5517865
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./1-move.py 7283904
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./1-move.py 7231788
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./1-move.py 3427537
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./1-move.py 6449647
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./2-infer.py /nn/6449647/20250121/CT/8 /nn/6449647/20250121/MR/7
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./1-move.py 2508411
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./2-infer.py /nn/2508411/20250121/CT/c /nn/2508411/20250121/MR/9
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./1-move.py 7154553
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./1-move.py 7253850
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./2-infer.py /nn/7253850/20250123/CT/b /nn/7253850/20250123/MR/8
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./1-move.py 7240437
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./2-infer.py /nn/7240437/20250123/CT/a /nn/7240437/20250123/MR/8
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./1-move.py 7239152
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./1-move.py 2957658
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./1-move.py 7295866
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./2-infer.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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nvidia-smi
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nvidia-smi
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nvidia-smi
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cd onlylian/
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ls
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python3 oar.py /nn/7295866/20250127/CT/a /nn/72/nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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ls /nn
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python3 oar.py /nn/7295866/20250127/CT/a /nn/72/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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copy oar.py oar2.py
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cp oar.py oar2.py
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dir /nn/7295866/
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dir /nn/7295866/20250127/
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dir /nn/7295866/20250127/nii/
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dir /nn/7295866/20250127/output/
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dir /nn/7295866/20250127/nii/
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dir /nn/7295866/20250127/input/
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dir /nn/7295866/20250127/output/
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dir /nn/7295866/20250127/CT/
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dir /nn/7295866/20250127/
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ls -lR /nn/7295866/20250127/
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cd onlylian/
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python test2.py
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python test2.py
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python test2.py
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ls /nn/7295866/20250127/output/processed_7_3D_SAG_T1_MPRAGE_+C_20250127132612.nii.gz
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ls /nn/7295866/20250127/output/processed_7_3D_SAG_T1_MPRAGE_+C_20250127132612.nii.gz
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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ls /nn/7295866/20250127/
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ls /nn/7295866/20250127/pyradise/
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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python test2.py
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apt install libxrender1
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python test2.py
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python test2.py
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python test2.py
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ls /nn/7295866/20250127/
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ls /nn/7295866/20250127/CT/
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python test2.py
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ls /nn/7295866/20250127/CT/
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ls -l /nn/7295866/20250127/CT/
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ls
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ls -ltr
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copy oar.py oar2.py
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cp oar.py oar2.py
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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ls /nn/7295866/20250127/CT/
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ls -ltr /nn/7295866/20250127/CT/
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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ls -ltr /nn/7295866/20250127/CT/
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ls -ltr /nn/7295866/20250127/CT/a-rtss*
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rm -ltr /nn/7295866/20250127/CT/a-rtss*
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rm /nn/7295866/20250127/CT/a-rtss*
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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rm -ltr /nn/7295866/20250127/CT/a-rtss*
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rm -ltr /nn/7295866/20250127/CT/
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ls /nn/7295866/20250127/CT/
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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ls /nn/7295866/20250127/CT/
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ls /nn/7295866/20250127/CT/7295866/
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ls -l /nn/7295866/20250127/CT/7295866/
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ls -l /nn/7295866/20250127/pyradise/
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ls -l /nn/7295866/20250127/pyradise/7295866/
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rm -rf /nn/7295866/20250127/pyradise/
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rm -rf /nn/7295866/20250127/pyradise
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rm -rf /nn/7295866/20250127/CT/7295866
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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ls /nn/7295866/20250127/pyradise
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ls /nn/7295866/20250127/pyradise
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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/nn/7295866/20250127/pyradise
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ls /nn/7295866/20250127/pyradise
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ls /nn/7295866/20250127/
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ls /nn/7295866/20250127/seg
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rm -rf /nn/7295866/20250127/seg
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ls /nn/7295866/20250127/
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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ls /nn/7295866/20250127/CT/a-rtss.dcm
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ls /nn/7295866/20250127/pyradise/
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python3 oar2.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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cp oar2.py oar3.py
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cd registration
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ls
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python best_reg.py
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cd ..
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python registration/best_reg.py
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python -m registration.best_reg
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python -m registration.best_reg
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python -m registration.best_reg
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python -m registration.best_reg
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python -m registration.best_reg
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cd onlylian/
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ls
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python -m registration.best_reg
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python -m registration.best_reg
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python -m registration.best_reg
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ls '/nn/7295866/20250127/nii/7_3D_SAG_T1_MPRAGE_+C_20250127132612_100.nii.gz'
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ls '/nn/7295866/20250127/nii/a_1.1_CyberKnife_head(MAR)_20250127111447.label.nii.gz'
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python -m registration.best_reg
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python -m registration.best_reg
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python -m registration.best_reg
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ls /nn/7295866/20250127/pyradise
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rm -rf /nn/7295866/20250127/pyradise
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python3 oar3.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
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ls nnUNet_results/Dataset222_OAR_TV/
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ls nnUNet_results/Dataset222_OAR_TV/nnUNetTrainer__nnUNetPlans__2d/
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ls nnUNet_results/Dataset222_OAR_TV/nnUNetTrainer__nnUNetPlans__2d/fold_0/
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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
|