FabianIsensee
commented
2 years ago Hi, it is very difficult to say what is going on without knowing more about the data and the trained models. How was your 5-fold CV result? Are the segmentations from the validation sets empty as well? Best, Fabian
mohannatd
Hello author,
I put my data set into the nnunet project and successfully preprocessed and trained, but the nii.gz result file obtained after reasoning is all black without segmentation results. What is the reason?
There are some information when reasoning. This model expects 1 input modalities for each image Found 28 unique case ids, here are some examples: ['test_7572.ni' 'test_7050.ni' 'test_7778.ni' 'test_6172.ni' 'test_6172.ni' 'test_6890.ni' 'test_6378.ni' 'test_6172.ni' 'test_6077.ni' 'test_6077.ni'] If they don't look right, make sure to double check your filenames. They must end with _0000.nii.gz etc number of cases: 28 number of cases that still need to be predicted: 28 emptying cuda cache loading parameters for folds, [0] I am not using the pre_train weight!! using the following model files: ['/home/three03/walyn/DATASET/nnFormer_trained_models/nnFormer/3d_fullres/Task11_PelvicTumour/nnFormerTrainerV2_PelvicTumour__nnFormerPlansv2.1/fold_0/model_best.model'] starting preprocessing generator starting prediction... preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_3051.ni.nii.gz using preprocessor GenericPreprocessor preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6077.ni.nii.gz using preprocessor GenericPreprocessor preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6172.ni.nii.gz using preprocessor GenericPreprocessor preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6285.ni.nii.gz using preprocessor GenericPreprocessor preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6378.ni.nii.gz using preprocessor GenericPreprocessor before crop: (1, 96, 128, 128) after crop: (1, 51, 38, 55) spacing: [0.75 4. 4. ]
no separate z, order 3 before crop: (1, 96, 128, 128) after crop: (1, 80, 41, 55) spacing: [0.65625 4. 4. ]
no separate z, order 3 before crop: (1, 96, 128, 128) after crop: (1, 49, 36, 61) spacing: [0.8125 4. 4. ]
no separate z, order 3 no separate z, order 1 no separate z, order 1 preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6494.ni.nii.gz using preprocessor GenericPreprocessor before: {'spacing': array([0.75, 4. , 4. ]), 'spacing_transposed': array([4. , 0.75, 4. ]), 'data.shape (data is transposed)': (1, 38, 51, 55)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 38, 48, 55)}
before: {'spacing': array([0.65625, 4. , 4. ]), 'spacing_transposed': array([4. , 0.65625, 4. ]), 'data.shape (data is transposed)': (1, 41, 80, 55)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 41, 65, 55)}
(1, 38, 48, 55) (1, 41, 65, 55) preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6890.ni.nii.gz using preprocessor GenericPreprocessor predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_3051.ni.nii.gz I am here !!! no separate z, order 1 preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6933.ni.nii.gz using preprocessor GenericPreprocessor before: {'spacing': array([0.8125, 4. , 4. ]), 'spacing_transposed': array([4. , 0.8125, 4. ]), 'data.shape (data is transposed)': (1, 36, 49, 61)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 36, 50, 61)}
before crop: (1, 96, 128, 128) after crop: (1, 59, 32, 59) spacing: [0.70833331 4. 4. ]
(1, 36, 50, 61) no separate z, order 3 no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 49, 35, 55) spacing: [0.86458331 4. 4. ]
before: {'spacing': array([0.70833331, 4. , 4. ]), 'spacing_transposed': array([4. , 0.70833331, 4. ]), 'data.shape (data is transposed)': (1, 32, 59, 59)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 32, 52, 59)}
no separate z, order 3 (1, 32, 52, 59) before crop: (1, 96, 128, 128) after crop: (1, 42, 32, 53) spacing: [0.86458331 4. 4. ]
no separate z, order 3 before crop: (1, 96, 128, 128) after crop: (1, 45, 28, 48) spacing: [0.92708331 4. 4. ]
no separate z, order 1 no separate z, order 3 before: {'spacing': array([0.86458331, 4. , 4. ]), 'spacing_transposed': array([4. , 0.86458331, 4. ]), 'data.shape (data is transposed)': (1, 35, 49, 55)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 35, 53, 55)}
(1, 35, 53, 55) no separate z, order 1 no separate z, order 1 before: {'spacing': array([0.86458331, 4. , 4. ]), 'spacing_transposed': array([4. , 0.86458331, 4. ]), 'data.shape (data is transposed)': (1, 32, 42, 53)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 32, 45, 53)}
(1, 32, 45, 53) before: {'spacing': array([0.92708331, 4. , 4. ]), 'spacing_transposed': array([4. , 0.92708331, 4. ]), 'data.shape (data is transposed)': (1, 28, 45, 48)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 28, 52, 48)}
(1, 28, 52, 48) before crop: (1, 96, 128, 128) after crop: (1, 61, 30, 47) spacing: [0.69791669 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.69791669, 4. , 4. ]), 'spacing_transposed': array([4. , 0.69791669, 4. ]), 'data.shape (data is transposed)': (1, 30, 61, 47)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 30, 53, 47)}
(1, 30, 53, 47) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6077.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6937.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 55, 35, 56) spacing: [0.84375 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.84375, 4. , 4. ]), 'spacing_transposed': array([4. , 0.84375, 4. ]), 'data.shape (data is transposed)': (1, 35, 55, 56)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 35, 58, 56)}
(1, 35, 58, 56) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6172.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6995.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 55, 32, 50) spacing: [0.86458331 4. 4. ]
no separate z, order 3 no separate z, order 1 True before: {'spacing': array([0.86458331, 4. , 4. ]), 'spacing_transposed': array([4. , 0.86458331, 4. ]), 'data.shape (data is transposed)': (1, 32, 55, 50)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 32, 59, 50)}
(1, 32, 59, 50) debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6285.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7050.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 51, 28, 47) spacing: [0.79166669 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.79166669, 4. , 4. ]), 'spacing_transposed': array([4. , 0.79166669, 4. ]), 'data.shape (data is transposed)': (1, 28, 51, 47)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 28, 50, 47)}
(1, 28, 50, 47) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6378.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7149.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 39, 38, 56) spacing: [0.88541669 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.88541669, 4. , 4. ]), 'spacing_transposed': array([4. , 0.88541669, 4. ]), 'data.shape (data is transposed)': (1, 38, 39, 56)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 38, 43, 56)}
(1, 38, 43, 56) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6890.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7114.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 53, 28, 43) spacing: [0.83333331 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.83333331, 4. , 4. ]), 'spacing_transposed': array([4. , 0.83333331, 4. ]), 'data.shape (data is transposed)': (1, 28, 53, 43)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 28, 55, 43)}
(1, 28, 55, 43) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6494.ni.nii.gz preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7234.ni.nii.gz I am here !!! using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 46, 32, 48) spacing: [0.78125 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.78125, 4. , 4. ]), 'spacing_transposed': array([4. , 0.78125, 4. ]), 'data.shape (data is transposed)': (1, 32, 46, 48)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 32, 45, 48)}
(1, 32, 45, 48) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7327.ni.nii.gz predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6933.ni.nii.gz I am here !!! using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 57, 35, 64) spacing: [0.69791669 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.69791669, 4. , 4. ]), 'spacing_transposed': array([4. , 0.69791669, 4. ]), 'data.shape (data is transposed)': (1, 35, 57, 64)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 35, 50, 64)}
(1, 35, 50, 64) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7418.ni.nii.gz using preprocessor GenericPreprocessor predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6937.ni.nii.gz I am here !!! force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 38, 29, 42) spacing: [0.91666669 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.91666669, 4. , 4. ]), 'spacing_transposed': array([4. , 0.91666669, 4. ]), 'data.shape (data is transposed)': (1, 29, 38, 42)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 29, 43, 42)}
(1, 29, 43, 42) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_6995.ni.nii.gz preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7498.ni.nii.gz I am here !!! using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 51, 26, 50) spacing: [0.76041669 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.76041669, 4. , 4. ]), 'spacing_transposed': array([4. , 0.76041669, 4. ]), 'data.shape (data is transposed)': (1, 26, 51, 50)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 26, 48, 50)}
(1, 26, 48, 50) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7050.ni.nii.gz preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7546.ni.nii.gz I am here !!! using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 51, 32, 53) spacing: [0.75 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.75, 4. , 4. ]), 'spacing_transposed': array([4. , 0.75, 4. ]), 'data.shape (data is transposed)': (1, 32, 51, 53)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 32, 48, 53)}
(1, 32, 48, 53) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7149.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7515.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 41, 36, 51) spacing: [1.34375 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([1.34375, 4. , 4. ]), 'spacing_transposed': array([4. , 1.34375, 4. ]), 'data.shape (data is transposed)': (1, 36, 41, 51)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 36, 69, 51)}
(1, 36, 69, 51) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7114.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7572.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 43, 28, 53) spacing: [0.9375 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.9375, 4. , 4. ]), 'spacing_transposed': array([4. , 0.9375, 4. ]), 'data.shape (data is transposed)': (1, 28, 43, 53)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 28, 50, 53)}
(1, 28, 50, 53) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7234.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7625.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 44, 27, 47) spacing: [0.86458331 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.86458331, 4. , 4. ]), 'spacing_transposed': array([4. , 0.86458331, 4. ]), 'data.shape (data is transposed)': (1, 27, 44, 47)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 27, 47, 47)}
(1, 27, 47, 47) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7662.ni.nii.gz using preprocessor GenericPreprocessor predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7327.ni.nii.gz I am here !!! force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 46, 26, 44) spacing: [0.8125 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.8125, 4. , 4. ]), 'spacing_transposed': array([4. , 0.8125, 4. ]), 'data.shape (data is transposed)': (1, 26, 46, 44)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 26, 47, 44)}
(1, 26, 47, 44) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7663.ni.nii.gz predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7418.ni.nii.gz I am here !!! using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 43, 29, 43) spacing: [0.92708331 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.92708331, 4. , 4. ]), 'spacing_transposed': array([4. , 0.92708331, 4. ]), 'data.shape (data is transposed)': (1, 29, 43, 43)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 29, 50, 43)}
(1, 29, 50, 43) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7498.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7756.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 43, 31, 47) spacing: [0.83333331 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.83333331, 4. , 4. ]), 'spacing_transposed': array([4. , 0.83333331, 4. ]), 'data.shape (data is transposed)': (1, 31, 43, 47)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 31, 45, 47)}
(1, 31, 45, 47) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7546.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7664.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 52, 27, 50) spacing: [0.78125 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.78125, 4. , 4. ]), 'spacing_transposed': array([4. , 0.78125, 4. ]), 'data.shape (data is transposed)': (1, 27, 52, 50)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 27, 51, 50)}
(1, 27, 51, 50) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7778.ni.nii.gz predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7515.ni.nii.gz I am here !!! using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 39, 28, 49) spacing: [0.9375 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.9375, 4. , 4. ]), 'spacing_transposed': array([4. , 0.9375, 4. ]), 'data.shape (data is transposed)': (1, 28, 39, 49)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 28, 46, 49)}
(1, 28, 46, 49) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7572.ni.nii.gz I am here !!! preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7997.ni.nii.gz using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [0 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 39, 31, 43) spacing: [1.66666663 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([1.66666663, 4. , 4. ]), 'spacing_transposed': array([4. , 1.66666663, 4. ]), 'data.shape (data is transposed)': (1, 31, 39, 43)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 31, 81, 43)}
(1, 31, 81, 43) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7625.ni.nii.gz preprocessing ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_8297.ni.nii.gz I am here !!! using preprocessor GenericPreprocessor force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 before crop: (1, 96, 128, 128) after crop: (1, 42, 30, 44) spacing: [0.88541669 4. 4. ]
no separate z, order 3 no separate z, order 1 before: {'spacing': array([0.88541669, 4. , 4. ]), 'spacing_transposed': array([4. , 0.88541669, 4. ]), 'data.shape (data is transposed)': (1, 30, 42, 44)} after: {'spacing': array([4. , 0.80208331, 4. ]), 'data.shape (data is resampled)': (1, 30, 46, 44)}
(1, 30, 46, 44) True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7662.ni.nii.gz I am here !!! force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7663.ni.nii.gz I am here !!! force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7756.ni.nii.gz I am here !!! force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7664.ni.nii.gz I am here !!! force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7778.ni.nii.gz I am here !!! force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_7997.ni.nii.gz I am here !!! force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done predicting ../DATASET/nnFormer_raw/nnFormer_raw_data/Task11_PelvicTumour/inferTs/output/test_8297.ni.nii.gz I am here !!! This worker has ended successfully, no errors to report force_separate_z: None interpolation order: 1 separate z: False lowres axis [0 2] no separate z, order 1 True debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 96, 128, 128) patch size: [ 96 128 128] steps (x, y, and z): [[0], [0], [0]] number of tiles: 1 prediction done This worker has ended successfully, no errors to report This worker has ended successfully, no errors to report This worker has ended successfully, no errors to report This worker has ended successfully, no errors to report This worker has ended successfully, no errors to report force_separate_z: None interpolation order: 1 separate z: False lowres axis [1 2] no separate z, order 1 inference done. Now waiting for the segmentation export to finish... WARNING! Cannot run postprocessing because the postprocessing file is missing. Make sure to run consolidate_folds in the output folder of the model first! The folder you need to run this in is /home/three03/walyn/DATASET/nnFormer_trained_models/nnFormer/3d_fullres/Task11_PelvicTumour/nnFormerTrainerV2_PelvicTumour__nnFormerPlansv2.1
Looking forward to your reply.