How to set parameters properly when using RandCropByPosNegLabeld and sliding_window_inference ?

[Moron9645]

Hi everyone,

I am currently trying to use the 3D U-net implemented by MONAI to segment liver out of a series of CT images.

After several trials I have got some result from the model. However, I am still confused about how to set the parameters properly in RandCropByPosNegLabeld (spatial_size, num_samples) and sliding_window_inference (roi_size, sw_batch_size).

As far as I am concerned, to make inputs possess the same shape, RandCropByPosNegLabeld randomly cuts the image into spatial_size size crops, num_samples would be the numbers of the crops. Should I set spatial_size according to the size of liver ?
For example, if the size of the liver is (250,200,150), should I set the spatial_size like (256,256,256) or (128,128,128) ? Of course I have tried directly with (250,200,150), but I got an error about tensor size dismatch then, why should I get this error ?

Also, as far as I am concerned, the sliding_window_inference make predictions with a sliding window going through all the images and predict the results, roi_size being the size of the windows, and sw_batch_size being the number of the windows (when I set sw_batch_size to 4, will there be 4 windows slidng at the same time ?). Then also the same problem, should I set spatial_size according to the size of liver and should all the three axis lengths be the same ?

Here I have listed the shapes, spacings, and liver sizes of all the images, which size should be proper to adapt to the spatial_size and roi_size ?

{'filename': 'liver_0.nii.gz', 'shape': (512, 512, 75), 'spacing': (0.7, 0.7, 5.0), 'after spacing': (360, 360, 375), 'liver': (216, 157, 145)}
{'filename': 'liver_1.nii.gz', 'shape': (512, 512, 123), 'spacing': (0.68, 0.68, 5.0), 'after spacing': (345, 345, 615), 'liver': (219, 168, 140)}
{'filename': 'liver_10.nii.gz', 'shape': (512, 512, 501), 'spacing': (0.77, 0.77, 1.0), 'after spacing': (394, 394, 501), 'liver': (240, 184, 180)}
{'filename': 'liver_100.nii.gz', 'shape': (512, 512, 685), 'spacing': (0.7, 0.7, 0.7), 'after spacing': (358, 358, 479), 'liver': (190, 195, 193)}
{'filename': 'liver_101.nii.gz', 'shape': (512, 512, 683), 'spacing': (0.71, 0.71, 0.7), 'after spacing': (361, 361, 478), 'liver': (225, 194, 181)}
{'filename': 'liver_102.nii.gz', 'shape': (512, 512, 677), 'spacing': (0.72, 0.72, 0.7), 'after spacing': (367, 367, 473), 'liver': (243, 217, 219)}
{'filename': 'liver_103.nii.gz', 'shape': (512, 512, 683), 'spacing': (0.86, 0.86, 0.7), 'after spacing': (438, 438, 478), 'liver': (207, 193, 146)}
{'filename': 'liver_104.nii.gz', 'shape': (512, 512, 781), 'spacing': (0.78, 0.78, 0.8), 'after spacing': (399, 399, 624), 'liver': (225, 150, 154)}
{'filename': 'liver_105.nii.gz', 'shape': (512, 512, 986), 'spacing': (0.84, 0.84, 0.7), 'after spacing': (432, 432, 690), 'liver': (205, 210, 167)}
{'filename': 'liver_106.nii.gz', 'shape': (512, 512, 771), 'spacing': (0.73, 0.73, 0.8), 'after spacing': (373, 373, 616), 'liver': (182, 158, 126)}
{'filename': 'liver_107.nii.gz', 'shape': (512, 512, 771), 'spacing': (0.78, 0.78, 0.8), 'after spacing': (400, 400, 616), 'liver': (223, 165, 182)}
{'filename': 'liver_108.nii.gz', 'shape': (512, 512, 856), 'spacing': (0.73, 0.73, 0.8), 'after spacing': (373, 373, 684), 'liver': (217, 223, 163)}
{'filename': 'liver_109.nii.gz', 'shape': (512, 512, 756), 'spacing': (0.76, 0.76, 0.8), 'after spacing': (390, 390, 604), 'liver': (208, 166, 154)}
{'filename': 'liver_11.nii.gz', 'shape': (512, 512, 466), 'spacing': (0.67, 0.67, 1.0), 'after spacing': (344, 344, 466), 'liver': (176, 187, 163)}
{'filename': 'liver_110.nii.gz', 'shape': (512, 512, 816), 'spacing': (0.72, 0.72, 0.8), 'after spacing': (368, 368, 652), 'liver': (201, 158, 152)}
{'filename': 'liver_111.nii.gz', 'shape': (512, 512, 761), 'spacing': (0.78, 0.78, 0.8), 'after spacing': (400, 400, 608), 'liver': (204, 229, 186)}
{'filename': 'liver_112.nii.gz', 'shape': (512, 512, 751), 'spacing': (0.64, 0.64, 0.8), 'after spacing': (327, 327, 600), 'liver': (200, 177, 152)}
{'filename': 'liver_113.nii.gz', 'shape': (512, 512, 836), 'spacing': (0.78, 0.78, 0.8), 'after spacing': (399, 399, 668), 'liver': (213, 196, 128)}
{'filename': 'liver_114.nii.gz', 'shape': (512, 512, 846), 'spacing': (0.78, 0.78, 0.8), 'after spacing': (400, 400, 676), 'liver': (226, 198, 172)}
{'filename': 'liver_115.nii.gz', 'shape': (512, 512, 846), 'spacing': (0.76, 0.76, 0.8), 'after spacing': (387, 387, 676), 'liver': (217, 193, 143)}
{'filename': 'liver_116.nii.gz', 'shape': (512, 512, 908), 'spacing': (0.79, 0.79, 0.7), 'after spacing': (404, 404, 635), 'liver': (195, 220, 153)}
{'filename': 'liver_117.nii.gz', 'shape': (512, 512, 836), 'spacing': (0.68, 0.68, 0.8), 'after spacing': (348, 348, 668), 'liver': (190, 179, 207)}
{'filename': 'liver_118.nii.gz', 'shape': (512, 512, 427), 'spacing': (0.74, 0.74, 1.5), 'after spacing': (381, 381, 640), 'liver': (216, 193, 183)}
{'filename': 'liver_119.nii.gz', 'shape': (512, 512, 461), 'spacing': (0.84, 0.84, 1.5), 'after spacing': (432, 432, 691), 'liver': (219, 199, 198)}
{'filename': 'liver_12.nii.gz', 'shape': (512, 512, 455), 'spacing': (0.65, 0.65, 1.0), 'after spacing': (335, 335, 455), 'liver': (221, 170, 189)}
{'filename': 'liver_120.nii.gz', 'shape': (512, 512, 424), 'spacing': (0.74, 0.74, 1.5), 'after spacing': (381, 381, 636), 'liver': (207, 164, 176)}
{'filename': 'liver_121.nii.gz', 'shape': (512, 512, 463), 'spacing': (0.79, 0.79, 1.5), 'after spacing': (407, 407, 694), 'liver': (190, 191, 165)}
{'filename': 'liver_122.nii.gz', 'shape': (512, 512, 422), 'spacing': (0.69, 0.69, 1.5), 'after spacing': (353, 353, 633), 'liver': (216, 155, 177)}
{'filename': 'liver_123.nii.gz', 'shape': (512, 512, 432), 'spacing': (0.75, 0.75, 1.5), 'after spacing': (383, 383, 648), 'liver': (249, 199, 170)}
{'filename': 'liver_124.nii.gz', 'shape': (512, 512, 407), 'spacing': (0.7, 0.7, 1.5), 'after spacing': (358, 358, 610), 'liver': (184, 141, 167)}
{'filename': 'liver_125.nii.gz', 'shape': (512, 512, 410), 'spacing': (0.71, 0.71, 1.5), 'after spacing': (365, 365, 615), 'liver': (209, 170, 164)}
{'filename': 'liver_126.nii.gz', 'shape': (512, 512, 401), 'spacing': (0.66, 0.66, 1.5), 'after spacing': (340, 340, 601), 'liver': (191, 164, 169)}
{'filename': 'liver_127.nii.gz', 'shape': (512, 512, 987), 'spacing': (0.77, 0.77, 0.7), 'after spacing': (395, 395, 690), 'liver': (196, 196, 153)}
{'filename': 'liver_128.nii.gz', 'shape': (512, 512, 654), 'spacing': (0.78, 0.78, 0.7), 'after spacing': (400, 400, 457), 'liver': (240, 204, 200)}
{'filename': 'liver_129.nii.gz', 'shape': (512, 512, 338), 'spacing': (0.71, 0.71, 0.7), 'after spacing': (361, 361, 236), 'liver': (271, 197, 194)}
{'filename': 'liver_13.nii.gz', 'shape': (512, 512, 605), 'spacing': (0.85, 0.85, 1.0), 'after spacing': (434, 434, 605), 'liver': (196, 205, 142)}
{'filename': 'liver_130.nii.gz', 'shape': (512, 512, 624), 'spacing': (0.68, 0.68, 0.7), 'after spacing': (350, 350, 436), 'liver': (197, 173, 169)}
{'filename': 'liver_14.nii.gz', 'shape': (512, 512, 588), 'spacing': (0.69, 0.69, 1.0), 'after spacing': (351, 351, 588), 'liver': (182, 192, 136)}
{'filename': 'liver_15.nii.gz', 'shape': (512, 512, 565), 'spacing': (0.65, 0.65, 1.0), 'after spacing': (335, 335, 565), 'liver': (177, 196, 130)}
{'filename': 'liver_16.nii.gz', 'shape': (512, 512, 689), 'spacing': (0.7, 0.7, 0.8), 'after spacing': (360, 360, 551), 'liver': (202, 175, 148)}
{'filename': 'liver_17.nii.gz', 'shape': (512, 512, 826), 'spacing': (0.74, 0.74, 0.8), 'after spacing': (381, 381, 660), 'liver': (174, 181, 156)}
{'filename': 'liver_18.nii.gz', 'shape': (512, 512, 845), 'spacing': (0.92, 0.92, 0.8), 'after spacing': (472, 472, 676), 'liver': (167, 177, 146)}
{'filename': 'liver_19.nii.gz', 'shape': (512, 512, 547), 'spacing': (0.75, 0.75, 0.8), 'after spacing': (385, 385, 437), 'liver': (190, 202, 147)}
{'filename': 'liver_2.nii.gz', 'shape': (512, 512, 517), 'spacing': (0.78, 0.78, 1.0), 'after spacing': (397, 397, 517), 'liver': (256, 190, 138)}
{'filename': 'liver_20.nii.gz', 'shape': (512, 512, 574), 'spacing': (0.8, 0.8, 0.8), 'after spacing': (411, 411, 459), 'liver': (215, 190, 155)}
{'filename': 'liver_21.nii.gz', 'shape': (512, 512, 437), 'spacing': (0.77, 0.77, 1.0), 'after spacing': (393, 393, 437), 'liver': (242, 186, 174)}
{'filename': 'liver_22.nii.gz', 'shape': (512, 512, 247), 'spacing': (0.98, 0.98, 3.27), 'after spacing': (499, 499, 807), 'liver': (156, 162, 147)}
{'filename': 'liver_23.nii.gz', 'shape': (512, 512, 391), 'spacing': (0.66, 0.66, 1.2), 'after spacing': (338, 338, 469), 'liver': (163, 165, 137)}
{'filename': 'liver_24.nii.gz', 'shape': (512, 512, 276), 'spacing': (0.67, 0.67, 1.5), 'after spacing': (343, 343, 414), 'liver': (158, 191, 177)}
{'filename': 'liver_25.nii.gz', 'shape': (512, 512, 601), 'spacing': (0.77, 0.77, 0.7), 'after spacing': (393, 393, 420), 'liver': (222, 137, 161)}
{'filename': 'liver_26.nii.gz', 'shape': (512, 512, 668), 'spacing': (0.86, 0.86, 0.7), 'after spacing': (442, 442, 467), 'liver': (211, 159, 134)}
{'filename': 'liver_27.nii.gz', 'shape': (512, 512, 861), 'spacing': (0.74, 0.74, 0.7), 'after spacing': (378, 378, 602), 'liver': (197, 144, 158)}
{'filename': 'liver_28.nii.gz', 'shape': (512, 512, 129), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 129), 'liver': (337, 267, 98)}
{'filename': 'liver_29.nii.gz', 'shape': (512, 512, 172), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 172), 'liver': (243, 210, 114)}
{'filename': 'liver_3.nii.gz', 'shape': (512, 512, 534), 'spacing': (0.69, 0.69, 1.0), 'after spacing': (355, 355, 534), 'liver': (182, 200, 169)}
{'filename': 'liver_30.nii.gz', 'shape': (512, 512, 200), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 200), 'liver': (266, 259, 119)}
{'filename': 'liver_31.nii.gz', 'shape': (512, 512, 91), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 91), 'liver': (227, 248, 67)}
{'filename': 'liver_32.nii.gz', 'shape': (512, 512, 139), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 139), 'liver': (263, 261, 116)}
{'filename': 'liver_33.nii.gz', 'shape': (512, 512, 135), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 135), 'liver': (247, 264, 95)}
{'filename': 'liver_34.nii.gz', 'shape': (512, 512, 151), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 151), 'liver': (341, 228, 98)}
{'filename': 'liver_35.nii.gz', 'shape': (512, 512, 124), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 124), 'liver': (433, 247, 116)}
{'filename': 'liver_36.nii.gz', 'shape': (512, 512, 111), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 111), 'liver': (240, 223, 83)}
{'filename': 'liver_37.nii.gz', 'shape': (512, 512, 122), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 122), 'liver': (260, 223, 98)}
{'filename': 'liver_38.nii.gz', 'shape': (512, 512, 132), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 132), 'liver': (274, 227, 94)}
{'filename': 'liver_39.nii.gz', 'shape': (512, 512, 260), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 260), 'liver': (296, 201, 239)}
{'filename': 'liver_4.nii.gz', 'shape': (512, 512, 841), 'spacing': (0.9, 0.9, 0.8), 'after spacing': (462, 462, 672), 'liver': (278, 206, 196)}
{'filename': 'liver_40.nii.gz', 'shape': (512, 512, 122), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 122), 'liver': (303, 280, 85)}
{'filename': 'liver_41.nii.gz', 'shape': (512, 512, 113), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 113), 'liver': (325, 203, 104)}
{'filename': 'liver_42.nii.gz', 'shape': (512, 512, 125), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 125), 'liver': (250, 197, 113)}
{'filename': 'liver_43.nii.gz', 'shape': (512, 512, 155), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 155), 'liver': (287, 304, 113)}
{'filename': 'liver_44.nii.gz', 'shape': (512, 512, 119), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 119), 'liver': (260, 277, 112)}
{'filename': 'liver_45.nii.gz', 'shape': (512, 512, 74), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 74), 'liver': (306, 258, 59)}
{'filename': 'liver_46.nii.gz', 'shape': (512, 512, 124), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 124), 'liver': (260, 212, 41)}
{'filename': 'liver_47.nii.gz', 'shape': (512, 512, 225), 'spacing': (1.0, 1.0, 1.0), 'after spacing': (512, 512, 225), 'liver': (261, 236, 83)}
{'filename': 'liver_48.nii.gz', 'shape': (512, 512, 244), 'spacing': (0.98, 0.98, 2.5), 'after spacing': (499, 499, 610), 'liver': (197, 214, 173)}
{'filename': 'liver_49.nii.gz', 'shape': (512, 512, 254), 'spacing': (0.96, 0.96, 2.5), 'after spacing': (489, 489, 635), 'liver': (184, 172, 180)}
{'filename': 'liver_5.nii.gz', 'shape': (512, 512, 537), 'spacing': (0.97, 0.97, 0.8), 'after spacing': (496, 496, 429), 'liver': (198, 209, 136)}
{'filename': 'liver_50.nii.gz', 'shape': (512, 512, 240), 'spacing': (0.91, 0.91, 2.5), 'after spacing': (464, 464, 600), 'liver': (203, 151, 158)}
{'filename': 'liver_51.nii.gz', 'shape': (512, 512, 227), 'spacing': (0.9, 0.9, 3.0), 'after spacing': (462, 462, 681), 'liver': (231, 217, 162)}
{'filename': 'liver_52.nii.gz', 'shape': (512, 512, 237), 'spacing': (0.84, 0.84, 2.5), 'after spacing': (428, 428, 592), 'liver': (174, 172, 138)}
{'filename': 'liver_53.nii.gz', 'shape': (512, 512, 105), 'spacing': (0.85, 0.85, 4.0), 'after spacing': (435, 435, 420), 'liver': (152, 174, 168)}
{'filename': 'liver_54.nii.gz', 'shape': (512, 512, 96), 'spacing': (0.83, 0.83, 5.0), 'after spacing': (424, 424, 480), 'liver': (207, 199, 145)}
{'filename': 'liver_55.nii.gz', 'shape': (512, 512, 192), 'spacing': (0.67, 0.67, 2.5), 'after spacing': (341, 341, 480), 'liver': (265, 150, 230)}
{'filename': 'liver_56.nii.gz', 'shape': (512, 512, 239), 'spacing': (0.8, 0.8, 2.0), 'after spacing': (410, 410, 478), 'liver': (237, 194, 180)}
{'filename': 'liver_57.nii.gz', 'shape': (512, 512, 366), 'spacing': (0.7, 0.7, 1.25), 'after spacing': (360, 360, 457), 'liver': (201, 176, 181)}
{'filename': 'liver_58.nii.gz', 'shape': (512, 512, 212), 'spacing': (0.68, 0.68, 2.0), 'after spacing': (350, 350, 424), 'liver': (236, 153, 166)}
{'filename': 'liver_59.nii.gz', 'shape': (512, 512, 216), 'spacing': (0.68, 0.68, 2.0), 'after spacing': (350, 350, 432), 'liver': (191, 164, 152)}
{'filename': 'liver_6.nii.gz', 'shape': (512, 512, 518), 'spacing': (0.87, 0.87, 1.0), 'after spacing': (447, 447, 518), 'liver': (236, 195, 185)}
{'filename': 'liver_60.nii.gz', 'shape': (512, 512, 244), 'spacing': (0.8, 0.8, 2.0), 'after spacing': (408, 408, 488), 'liver': (275, 218, 158)}
{'filename': 'liver_61.nii.gz', 'shape': (512, 512, 193), 'spacing': (0.76, 0.76, 2.5), 'after spacing': (387, 387, 482), 'liver': (252, 185, 152)}
{'filename': 'liver_62.nii.gz', 'shape': (512, 512, 188), 'spacing': (0.64, 0.64, 2.0), 'after spacing': (329, 329, 376), 'liver': (177, 137, 176)}
{'filename': 'liver_63.nii.gz', 'shape': (512, 512, 104), 'spacing': (0.74, 0.74, 5.0), 'after spacing': (378, 378, 520), 'liver': (188, 174, 185)}
{'filename': 'liver_64.nii.gz', 'shape': (512, 512, 230), 'spacing': (0.78, 0.78, 2.0), 'after spacing': (398, 398, 460), 'liver': (207, 187, 206)}
{'filename': 'liver_65.nii.gz', 'shape': (512, 512, 513), 'spacing': (0.62, 0.62, 0.8), 'after spacing': (320, 320, 409), 'liver': (183, 125, 160)}
{'filename': 'liver_66.nii.gz', 'shape': (512, 512, 86), 'spacing': (0.71, 0.71, 5.0), 'after spacing': (365, 365, 430), 'liver': (192, 191, 175)}
{'filename': 'liver_67.nii.gz', 'shape': (512, 512, 165), 'spacing': (0.71, 0.71, 2.5), 'after spacing': (364, 364, 412), 'liver': (192, 144, 195)}
{'filename': 'liver_68.nii.gz', 'shape': (512, 512, 266), 'spacing': (0.67, 0.67, 2.5), 'after spacing': (341, 341, 664), 'liver': (214, 167, 158)}
{'filename': 'liver_69.nii.gz', 'shape': (512, 512, 245), 'spacing': (0.75, 0.75, 2.0), 'after spacing': (386, 386, 490), 'liver': (190, 199, 186)}
{'filename': 'liver_7.nii.gz', 'shape': (512, 512, 541), 'spacing': (0.75, 0.75, 1.0), 'after spacing': (383, 383, 541), 'liver': (236, 191, 175)}
{'filename': 'liver_70.nii.gz', 'shape': (512, 512, 333), 'spacing': (0.6, 0.6, 1.25), 'after spacing': (305, 305, 416), 'liver': (228, 138, 138)}
{'filename': 'liver_71.nii.gz', 'shape': (512, 512, 94), 'spacing': (0.56, 0.56, 5.0), 'after spacing': (285, 285, 470), 'liver': (182, 170, 180)}
{'filename': 'liver_72.nii.gz', 'shape': (512, 512, 93), 'spacing': (0.68, 0.68, 2.5), 'after spacing': (346, 346, 232), 'liver': (177, 191, 145)}
{'filename': 'liver_73.nii.gz', 'shape': (512, 512, 121), 'spacing': (0.95, 0.95, 4.0), 'after spacing': (487, 487, 484), 'liver': (193, 213, 196)}
{'filename': 'liver_74.nii.gz', 'shape': (512, 512, 107), 'spacing': (0.83, 0.83, 5.0), 'after spacing': (423, 423, 535), 'liver': (263, 225, 160)}
{'filename': 'liver_75.nii.gz', 'shape': (512, 512, 89), 'spacing': (0.76, 0.76, 5.0), 'after spacing': (388, 388, 445), 'liver': (198, 163, 185)}
{'filename': 'liver_76.nii.gz', 'shape': (512, 512, 168), 'spacing': (0.74, 0.74, 2.5), 'after spacing': (380, 380, 420), 'liver': (209, 188, 185)}
{'filename': 'liver_77.nii.gz', 'shape': (512, 512, 94), 'spacing': (0.78, 0.78, 5.0), 'after spacing': (399, 399, 470), 'liver': (189, 207, 170)}
{'filename': 'liver_78.nii.gz', 'shape': (512, 512, 198), 'spacing': (0.79, 0.79, 2.5), 'after spacing': (401, 401, 495), 'liver': (193, 179, 148)}
{'filename': 'liver_79.nii.gz', 'shape': (512, 512, 147), 'spacing': (0.8, 0.8, 3.0), 'after spacing': (408, 408, 441), 'liver': (170, 182, 177)}
{'filename': 'liver_8.nii.gz', 'shape': (512, 512, 541), 'spacing': (0.85, 0.85, 1.0), 'after spacing': (434, 434, 541), 'liver': (212, 187, 178)}
{'filename': 'liver_80.nii.gz', 'shape': (512, 512, 217), 'spacing': (0.68, 0.68, 2.0), 'after spacing': (350, 350, 434), 'liver': (195, 148, 152)}
{'filename': 'liver_81.nii.gz', 'shape': (512, 512, 343), 'spacing': (0.7, 0.7, 1.25), 'after spacing': (360, 360, 428), 'liver': (219, 157, 139)}
{'filename': 'liver_82.nii.gz', 'shape': (512, 512, 519), 'spacing': (0.62, 0.62, 0.8), 'after spacing': (320, 320, 415), 'liver': (225, 170, 136)}
{'filename': 'liver_83.nii.gz', 'shape': (512, 512, 871), 'spacing': (0.74, 0.74, 0.7), 'after spacing': (380, 380, 609), 'liver': (218, 136, 151)}
{'filename': 'liver_84.nii.gz', 'shape': (512, 512, 733), 'spacing': (0.76, 0.76, 0.7), 'after spacing': (388, 388, 513), 'liver': (219, 225, 177)}
{'filename': 'liver_85.nii.gz', 'shape': (512, 512, 630), 'spacing': (0.64, 0.64, 0.7), 'after spacing': (330, 330, 440), 'liver': (199, 184, 193)}
{'filename': 'liver_86.nii.gz', 'shape': (512, 512, 647), 'spacing': (0.68, 0.68, 0.7), 'after spacing': (350, 350, 452), 'liver': (169, 193, 184)}
{'filename': 'liver_87.nii.gz', 'shape': (512, 512, 896), 'spacing': (0.85, 0.85, 0.8), 'after spacing': (437, 437, 716), 'liver': (256, 233, 171)}
{'filename': 'liver_88.nii.gz', 'shape': (512, 512, 811), 'spacing': (0.76, 0.76, 0.8), 'after spacing': (387, 387, 648), 'liver': (220, 189, 140)}
{'filename': 'liver_89.nii.gz', 'shape': (512, 512, 766), 'spacing': (0.64, 0.64, 0.8), 'after spacing': (326, 326, 612), 'liver': (233, 170, 153)}
{'filename': 'liver_9.nii.gz', 'shape': (512, 512, 549), 'spacing': (0.82, 0.82, 1.0), 'after spacing': (420, 420, 549), 'liver': (234, 175, 172)}
{'filename': 'liver_90.nii.gz', 'shape': (512, 512, 751), 'spacing': (0.78, 0.78, 0.8), 'after spacing': (399, 399, 600), 'liver': (186, 210, 146)}
{'filename': 'liver_91.nii.gz', 'shape': (512, 512, 751), 'spacing': (0.86, 0.86, 0.8), 'after spacing': (439, 439, 600), 'liver': (208, 219, 151)}
{'filename': 'liver_92.nii.gz', 'shape': (512, 512, 836), 'spacing': (0.67, 0.67, 0.8), 'after spacing': (343, 343, 668), 'liver': (200, 179, 143)}
{'filename': 'liver_93.nii.gz', 'shape': (512, 512, 696), 'spacing': (0.66, 0.66, 0.8), 'after spacing': (338, 338, 556), 'liver': (220, 162, 176)}
{'filename': 'liver_94.nii.gz', 'shape': (512, 512, 917), 'spacing': (0.84, 0.84, 0.7), 'after spacing': (429, 429, 641), 'liver': (177, 201, 175)}
{'filename': 'liver_95.nii.gz', 'shape': (512, 512, 841), 'spacing': (0.74, 0.74, 0.8), 'after spacing': (377, 377, 672), 'liver': (250, 148, 211)}
{'filename': 'liver_96.nii.gz', 'shape': (512, 512, 722), 'spacing': (0.75, 0.75, 0.7), 'after spacing': (382, 382, 505), 'liver': (219, 191, 209)}
{'filename': 'liver_97.nii.gz', 'shape': (512, 512, 671), 'spacing': (0.72, 0.72, 0.7), 'after spacing': (370, 370, 469), 'liver': (232, 208, 161)}
{'filename': 'liver_98.nii.gz', 'shape': (512, 512, 645), 'spacing': (0.73, 0.73, 0.7), 'after spacing': (376, 376, 451), 'liver': (196, 186, 164)}
{'filename': 'liver_99.nii.gz', 'shape': (512, 512, 629), 'spacing': (0.78, 0.78, 0.7), 'after spacing': (400, 400, 440), 'liver': (197, 185, 157)}

Thanks a lot in advance !!

[ghost]

Hi,
I'm not part of the MONAI team but have overcome some of these problems so thought I'd try to help.
Setting the spatial size for the crop: I don't have a definitive answer but my take is that how well the features are picked up will depend at least a little on the anatomy, I don't work on the liver but think you could try different volume sizes and compare. Smaller volumes will of course run faster so perhaps it may work well to have smaller volumes and set a larger value for num_samples to get more cropped volumes?
Yes, I too had problems getting an error for the spatial size. I previously asked a question about this but the answer was not definitive. Basically some values work and others don't and I don't exactly know the math behind it. For me it took some trial and error and now usually stick to values values of 32, 64, 96, 192, 288.
I'd be interested to hear answers for the sliding window

[Nic-Ma]

Hi @Moron9645 ,

1. Yes, sw_batch_size is the windows running in parallel.
2. spatial_size not need to set all the three axis lengths be the same, you can try any size you want, just make sure don't out of memory.
3. RandCropByPosNegLabeld is usually used during training to generate random patches, SlidingWindow is usually used in validation.

Thanks.

[Vivekrpg]

How does the this information get generated?

{'filename': 'liver_0.nii.gz', 'shape': (512, 512, 75), 'spacing': (0.7, 0.7, 5.0), 'after spacing': (360, 360, 375), 'liver': (216, 157, 145)}

I am looking to print the filename when my dataloader is working on. How do i do that?

[rijobro]

How about something like this (untested)?:

def print_fname(data):
    print(data["filename"])
    return data

transforms = Compose([
    ...,
    Lambda(print_fname),
    ...,
])

Not sure you'll get useful output if num_workers>1 though.

[Vivekrpg]

Yes, it doesn't give accurate names when num_workers > 1. Although not essential, but is useful to debug sometimes.