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upload to new server
2025-02-01 07:57:22 +00:00
python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
export nnUNet_results=/123/onlylian/nnUNet_results
export nnUNet_preprocessed=/123/onlylian/nnUNet_preprocessed
export nnUNet_results=/123/onlylian/nnUNet_results
cd /123/onlylian/nnUNet_results
ls -l
ls -l Dataset505
python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
cd ..
python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
export nnUNet_raw="/onlylian/nnUNet_raw"
export nnUNet_preprocessed="/onlylian/nnUNet_preprocessed"
export nnUNet_results="/onlylian/nnUNet_results"
echo $nnUNet_raw
echo $nnUNet_preprocessed
echo $nnUNet_results
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
nnUNetv2_predict -i /nn/7208298/20241213/input -o /nn/7208298/20241213/output -d 505 -c 3d_fullres -f 0 -tr nnUNetTrainer -p nnUNetPlans
ls -l /onlylian/nnUNet_results
ls -l /onlylian/nnUNet_raw
python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
/nn/7208298/20241213/output
ls -l /nn/7208298/20241213/output
cat /nn/7208298/20241213/output/[filename]
cp -r /nn/7208298/20241213/output ./onlylian
cp -r /nn/7208298/20241213/output ./onlylian
cp -r /nn/7208298/20241213/input ./onlylian
Initial commit
2023-08-08 22:04:06 +00:00
upload to new server
2025-02-01 07:57:22 +00:00
python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
cp -r /nn/7208298/20241213/output ./onlylian
python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
cp -r /nn/7208298/20241213/output ./onlylian
python3 oar.py /nn/2783853/20241217/CT/9 /nn/2783853/20241217/MR/8
python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
cp -r /nn/7208298/20241213/output ./onlylian
python3 oar.py /nn/2783853/20241217/CT/9 /nn/2783853/20241217/MR/
python3 oar.py /nn/4608443/20241219/CT/a /nn/4608443/20241219/MR/7
python3 oar.py /nn/7208298/20241213/CT/a /nn/7208298/20241213/MR/7
cp -r /nn/7208298/20241213/output ./onlylian
python3 oar.py /nn/5108920/20241223/CT/a /nn/5108920/20241223/MR/7
python3 oar.py /nn/5435462/20241224/CT/9 /nn/5435462/20241224/MR/7
python3 oar.py /nn/2944822/20241224/CT/e /nn/2944822/20241224/MR/9
python3 oar.py /nn/7287366/20241225/CT/9 /nn/7287366/20241225/MR/7
python3 oar.py /nn/6405610/20241225/CT/9 /nn/6405610/20241225/MR/7
python3 oar.py /nn/7286032/20241226/CT/b /nn/7286032/20241226/MR/9
python3 oar.py /nn/1786330/20241226/CT/b /nn/1786330/20241226/MR/8
python3 oar.py /nn/7284108/20241227/CT/b /nn/7284108/20241227/MR/8
python3 oar.py /nn/4365592/20241227/CT/a /nn/4365592/20241227/MR/7
python3 oar.py /nn/2367245/20241223/CT/b /nn/2367245/20241231/MR/7
python3 oar.py /nn/3018505/20250102/CT/9 /nn/3018505/20250102/MR/8
python3 oar.py /nn/6827885/20250102/CT/a /nn/6827885/20250102/MR/7
python3 oar.py /nn/2556090/20250103/CT/a /nn/2556090/20250103/MR/7
python3 oar.py /nn/6902522/20250103/CT/a /nn/6902522/20250103/MR/7
python3 oar.py /nn/5908183/20250106/CT/a /nn/5908183/20250106/MR/7
python3 oar.py /nn/7165972/20250106/CT/a /nn/7165972/20250106/MR/7
python3 oar.py /nn/6248872/20250108/CT/a /nn/6248872/20250108/MR/8
python3 oar.py /nn/7223127/20250108/CT/a /nn/7223127/20250108/MR/6
python3 oar.py /nn/4398001/20250114/CT/9 /nn/4398001/20250114/MR/7
python3 oar.py /nn/4003636/20250114/CT/9 /nn/4003636/20250114/MR/8
python3 oar.py /nn/5131302/20250116/CT/9 /nn/5131302/20250116/MR/7
python3 oar.py /nn/5337151/20250116/CT/9 /nn/5337151/20250103/MR/b
python3 oar.py /nn/7283904/20250116/CT/9 /nn/7283904/20250116/MR/7
python3 oar.py /nn/5517865/20250117/CT/a /nn/5517865/20250117/MR/8
python3 oar.py /nn/7231788/20250120/CT/a /nn/7231788/20250120/MR/8
python3 oar.py /nn/3427537/20250120/CT/a /nn/3427537/20250120/MR/8
python3 oar.py /nn/7154553/20250122/CT/9 /nn/7154553/20250122/MR/7
python3 oar.py /nn/7239152/20250124/CT/a /nn/7239152/20250124/MR/7
python3 oar.py /nn/2957658/20250124/CT/b /nn/2957658/20250124/MR/8
python3 oar.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
python3 oar.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
python3 oar.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
conda env list
ls -l
python oar.py /nn/7295866/20250127/CT/a /nn/7295866/20250127/MR/7
./1-move.py 4608443
Initial commit
2023-08-08 22:04:06 +00:00
./1-move.py 1561614
upload to new server
2025-02-01 07:57:22 +00:00
./2-infer.py /nn/1561614/20241220/CT/a /nn/1561614/20241220/MR/8
./1-move.py 2641998
./2-infer.py /nn/2641998/20241220/CT/c /nn/2641998/20241220/MR/3
./1-move.py 5108920
./1-move.py 5435462
./1-move.py 2944822
./1-move.py 7287366
./1-move.py 6405610
./1-move.py 7286032
./1-move.py 1786330
./1-move.py 7284108
./1-move.py 7365592
./1-move.py 4365592
./1-move.py 6901803
./2-infer.py /nn/6901803/20241230/CT/9 /nn/6901803/20241230/MR/8
Initial commit
2023-08-08 22:04:06 +00:00
./1-move.py 7146030
upload to new server
2025-02-01 07:57:22 +00:00
./2-infer.py /nn/7146030/20241230/CT/b /nn/7146030/20241230/MR/8
./1-move.py 3560986
./2-infer.py /nn/3560986/20241231/CT/9 /nn/3560986/20241231/MR/8
./1-move.py 6075924
./2-infer.py /nn/6075924/20241231/CT/a /nn/6075924/20241231/MR/8
./1-move.py 2367245
./2-infer.py /nn/2367245/20241223/CT/b /nn/2367245/20241231/MR/7
./1-move.py 2367245
./1-move.py 3018505
./1-move.py 6827885
./1-move.py 2556090
./1-move.py 6902522
./1-move.py 5908183
./1-move.py 7165972
./1-move.py 5835974
./2-infer.py /nn/5835974/20250107/CT/9 /nn/5835974/20250107/MR/7
./1-move.py 7239182
Initial commit
2023-08-08 22:04:06 +00:00
upload to new server
2025-02-01 07:57:22 +00:00
./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
Initial commit
2023-08-08 22:04:06 +00:00
ps aux
upload to new server
2025-02-01 07:57:22 +00:00
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
Initial commit
2023-08-08 22:04:06 +00:00
nvidia-smi
upload to new server
2025-02-01 07:57:22 +00:00
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
Initial commit
2023-08-08 22:04:06 +00:00
nvidia-smi
upload to new server
2025-02-01 07:57:22 +00:00
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
Initial commit
2023-08-08 22:04:06 +00:00
nvidia-smi
upload to new server
2025-02-01 07:57:22 +00:00
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
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