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Brain tumor segmentation for MICCAI 2017 BraTS challenge

License: BSD 3-Clause "New" or "Revised" License

Python 97.13% Shell 2.87%

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poornasandur hefeicyp qianyeyang kkfuwfny lxmwust mohammedsamir77 yf817 nadia18alam faustomilletari mingrui peterxiaoguo liucong-1 deeplearninginmedicine qzane bcit-socas jcd-gh ck37 donghaozhang mschikay magsonnerlind julclu jomine94 pingaowang nojuman liu3xing3long mohamedheshammustafa tangyuan5833 nbekele melodylail trane293 afcarl htylab chitrita andreale28 rajshah9914 wyli picspin zpeng1989 huangpu1 hymedc stephanmeesters calmscout pranavkantgaur johnnychhsu amzpotato xiaochengcike guohan950106 tenround forkacc jacksu20160407 mufarooqq iamyashasvi prativa peanut1022 ieee820 thejhacker abnerxzhe gurpreetsingh9465 9lena1 hfhust fhxzh xzllxls desperado11 kingshukmitra333 shijial chetanmadan aliscifp elites2017 tejaswikapoor tianqwang junaid199f sweta271097 ajoshiusc pseudonerd zhanglang1860 steven0203 gucheng123 pigen01 thnkim databloom pratiksavla ispz redfish41 ljljlj02 singh-ap devhliu sunshiqisky zhongliangxue keepersecond liuhui123521 gunju gusleo brain-tumor yangyuren03 russchua tor4z liuwenhaha jackyysu ramarabah ajinkyajawale14499

brats17's Issues

Missing appropriate orientation and origin for prediction results

When running test.py the saved prediction results are missing appropriate orientation and origin since the output files are initiated with eye(4). This will cause issues when viewing the image data and the segmentation masks in most viewing software. Suggestion would be to remember the orientation and origin from the image volumes and to use this when initiating the output files, e.g. use img.get_affine() when reading the image data.

Regarding subimage patch and label size

Hi,

I was curious as to how you have selected sub-image patch size of [19, 144, 144, 4]? Is it based on cross-validation? Further as already asked here: (#20) , why the corresponding label has 11 units along depth? [11, 144, 144, 1] as opposed to 19 in input sample?

,,,.

Version of tensorflow

Hi Guotai Wang,

Thank you for sharing this DL model. I would like to try it on my dataset but I guess it is not compatible with the last versions tensorflow and a bug is raised while reading model17/msnet_wt32_20000.ckpt.
Which version were you using?

Best,
TD

With the latest versions I get this error:

 Not found: Key MSkNet_WT32/block1_1/bn_0/MSkNet_WT32/block1_1/bn_0/moving_mean/biased not found in checkpoint

With 1.4:

INFO:niftynet: Restoring parameters from model17/msnet_wt32_20000.ckpt
2018-06-07 16:49:03.616332: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_0/gamma not found in checkpoint
2018-06-07 16:49:03.616678: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_1/MSkNet_WT32/block2_2/bn_1/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.617552: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_1/MSkNet_WT32/block2_2/bn_1/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.617906: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_1/MSkNet_WT32/block2_2/bn_1/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.618965: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_0/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.618705: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_0/beta not found in checkpoint
2018-06-07 16:49:03.623919: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_1/beta not found in checkpoint
2018-06-07 16:49:03.624665: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_1/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.626079: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_1/MSkNet_WT32/block2_2/bn_1/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.626261: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/conv_0/w not found in checkpoint
2018-06-07 16:49:03.626513: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_0/MSkNet_WT32/block2_2/bn_0/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.627413: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_0/moving_variance not found in check                  point
2018-06-07 16:49:03.628693: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_1/gamma not found in checkpoint
2018-06-07 16:49:03.629983: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/prelu_acti_0/alpha not found in checkpo                  int
2018-06-07 16:49:03.630295: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/conv_1/w not found in checkpoint
2018-06-07 16:49:03.632065: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_0/MSkNet_WT32/block3_1/bn_0/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.632458: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_0/MSkNet_WT32/block3_1/bn_0/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.633083: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_1/moving_variance not found in check                  point
2018-06-07 16:49:03.638673: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_0/MSkNet_WT32/block3_1/bn_0/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.639369: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_0/MSkNet_WT32/block3_1/bn_0/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.639891: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_0/gamma not found in checkpoint
2018-06-07 16:49:03.644504: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_1/MSkNet_WT32/block3_1/bn_1/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.644617: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_1/MSkNet_WT32/block3_1/bn_1/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.644986: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_0/MSkNet_WT32/block2_2/bn_0/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.645386: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_0/beta not found in checkpoint
2018-06-07 16:49:03.645500: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_0/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.645594: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_0/moving_variance not found in check                  point
2018-06-07 16:49:03.646415: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/prelu_acti_1/alpha not found in checkpo                  int
2018-06-07 16:49:03.647268: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_1/MSkNet_WT32/block3_1/bn_1/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.647428: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_1/MSkNet_WT32/block3_1/bn_1/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.652710: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_0/MSkNet_WT32/block2_2/bn_0/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.656456: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/conv_1/w not found in checkpoint
2018-06-07 16:49:03.657478: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_1/beta not found in checkpoint
2018-06-07 16:49:03.658787: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_2/bn_0/MSkNet_WT32/block2_2/bn_0/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.659074: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/prelu_acti_0/alpha not found in checkpo                  int
2018-06-07 16:49:03.659387: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_1/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.661465: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_1/moving_variance not found in check                  point
2018-06-07 16:49:03.661853: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/conv_0/w not found in checkpoint
2018-06-07 16:49:03.662154: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_0/MSkNet_WT32/block3_2/bn_0/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.662321: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/prelu_acti_1/alpha not found in checkpo                  int
2018-06-07 16:49:03.664620: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_0/MSkNet_WT32/block3_2/bn_0/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.662552: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/prelu_acti_1/alpha not found in checkpo                  int
2018-06-07 16:49:03.664830: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_0/MSkNet_WT32/block3_2/bn_0/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.665621: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_1/bn_1/gamma not found in checkpoint
2018-06-07 16:49:03.668703: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_0/beta not found in checkpoint
2018-06-07 16:49:03.668865: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_0/moving_variance not found in check                  point
2018-06-07 16:49:03.669127: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_0/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.669505: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_0/MSkNet_WT32/block3_2/bn_0/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.677448: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_0/gamma not found in checkpoint
2018-06-07 16:49:03.681224: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/prelu_acti_0/alpha not found in checkpo                  int
2018-06-07 16:49:03.681457: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_1/MSkNet_WT32/block3_2/bn_1/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.681849: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_1/beta not found in checkpoint
2018-06-07 16:49:03.682017: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_1/MSkNet_WT32/block3_2/bn_1/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.682982: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_1/MSkNet_WT32/block3_2/bn_1/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.683272: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_1/MSkNet_WT32/block3_2/bn_1/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.687461: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_1/gamma not found in checkpoint
2018-06-07 16:49:03.687882: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_1/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.689927: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/prelu_acti_0/alpha not found in checkpo                  int
2018-06-07 16:49:03.689392: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/conv_1/w not found in checkpoint
2018-06-07 16:49:03.690053: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/conv_0/w not found in checkpoint
2018-06-07 16:49:03.690486: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/prelu_acti_1/alpha not found in checkpo                  int
2018-06-07 16:49:03.692057: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/bn_1/moving_variance not found in check                  point
2018-06-07 16:49:03.692639: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_0/MSkNet_WT32/block3_3/bn_0/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.697279: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_0/beta not found in checkpoint
2018-06-07 16:49:03.700296: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_0/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.700720: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_0/MSkNet_WT32/block3_3/bn_0/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.701270: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_0/gamma not found in checkpoint
2018-06-07 16:49:03.702623: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/conv_0/w not found in checkpoint
2018-06-07 16:49:03.703024: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_0/moving_variance not found in check                  point
2018-06-07 16:49:03.703428: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_0/MSkNet_WT32/block3_3/bn_0/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.706216: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_0/MSkNet_WT32/block3_3/bn_0/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.706852: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_1/MSkNet_WT32/block3_3/bn_1/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.711187: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_1/beta not found in checkpoint
2018-06-07 16:49:03.712626: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_1/gamma not found in checkpoint
2018-06-07 16:49:03.713066: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_1/MSkNet_WT32/block3_3/bn_1/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.713305: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_1/MSkNet_WT32/block3_3/bn_1/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.713846: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_1/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.713915: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_2/conv_1/w not found in checkpoint
2018-06-07 16:49:03.714199: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_1/MSkNet_WT32/block3_3/bn_1/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.714363: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_1/moving_variance not found in check                  point
2018-06-07 16:49:03.721599: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/conv_0/w not found in checkpoint
2018-06-07 16:49:03.721953: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_0/MSkNet_WT32/block4_1/bn_0/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.723133: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/bn_1/moving_variance not found in check                  point
2018-06-07 16:49:03.723995: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/prelu_acti_1/alpha not found in checkpo                  int
2018-06-07 16:49:03.724339: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_1/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.726725: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/prelu_acti_0/alpha not found in checkpo                  int
2018-06-07 16:49:03.727709: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_0/MSkNet_WT32/block4_1/bn_0/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.728160: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_0/beta not found in checkpoint
2018-06-07 16:49:03.728698: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_1/gamma not found in checkpoint
2018-06-07 16:49:03.729893: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block3_3/conv_1/w not found in checkpoint
2018-06-07 16:49:03.732808: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_0/MSkNet_WT32/block4_1/bn_0/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.734627: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_1/beta not found in checkpoint
2018-06-07 16:49:03.735007: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_0/gamma not found in checkpoint
2018-06-07 16:49:03.733931: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_0/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.735558: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_1/MSkNet_WT32/block4_1/bn_1/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.738595: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_1/MSkNet_WT32/block4_1/bn_1/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.738693: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_0/MSkNet_WT32/block4_1/bn_0/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.744221: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_1/MSkNet_WT32/block2_1/bn_1/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.744445: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_1/gamma not found in checkpoint
2018-06-07 16:49:03.744578: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_0/moving_variance not found in check                  point
2018-06-07 16:49:03.744718: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_1/MSkNet_WT32/block4_1/bn_1/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.744950: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_1/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.745131: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_1/beta not found in checkpoint
2018-06-07 16:49:03.746840: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_1/MSkNet_WT32/block4_1/bn_1/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.748906: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_1/MSkNet_WT32/block2_1/bn_1/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.750169: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/bn_1/moving_variance not found in check                  point
2018-06-07 16:49:03.750952: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/conv_0/w not found in checkpoint
2018-06-07 16:49:03.751980: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/conv_1/w not found in checkpoint
2018-06-07 16:49:03.751696: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/prelu_acti_1/alpha not found in checkpo                  int
2018-06-07 16:49:03.752055: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_0/MSkNet_WT32/block4_2/bn_0/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.760392: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_0/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.760788: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_0/beta not found in checkpoint
2018-06-07 16:49:03.761721: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_0/MSkNet_WT32/block4_2/bn_0/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.762526: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_0/gamma not found in checkpoint
2018-06-07 16:49:03.762861: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_1/prelu_acti_0/alpha not found in checkpo                  int
2018-06-07 16:49:03.763231: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_0/MSkNet_WT32/block4_2/bn_0/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.767323: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_1/MSkNet_WT32/block4_2/bn_1/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.769900: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_0/moving_variance not found in check                  point
2018-06-07 16:49:03.770570: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_1/MSkNet_WT32/block4_2/bn_1/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.770104: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_1/MSkNet_WT32/block4_2/bn_1/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.770641: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_1/MSkNet_WT32/block2_1/bn_1/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.769975: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_0/MSkNet_WT32/block4_2/bn_0/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.771322: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_1/MSkNet_WT32/block4_2/bn_1/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.771612: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_1/gamma not found in checkpoint
2018-06-07 16:49:03.777855: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/conv_0/w not found in checkpoint
2018-06-07 16:49:03.778512: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/conv_1/w not found in checkpoint
2018-06-07 16:49:03.778821: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_1/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.779643: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_1/MSkNet_WT32/block2_1/bn_1/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.780069: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/prelu_acti_1/alpha not found in checkpo                  int
2018-06-07 16:49:03.783007: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_0/MSkNet_WT32/block4_3/bn_0/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.783500: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_1/beta not found in checkpoint
2018-06-07 16:49:03.784454: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/bn_1/moving_variance not found in check                  point
2018-06-07 16:49:03.784788: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_0/MSkNet_WT32/block4_3/bn_0/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.785046: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_0/MSkNet_WT32/block4_3/bn_0/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.789530: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_0/MSkNet_WT32/block4_3/bn_0/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.790392: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_0/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.792572: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_0/moving_variance not found in check                  point
2018-06-07 16:49:03.793200: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_0/beta not found in checkpoint
2018-06-07 16:49:03.793507: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_1/MSkNet_WT32/block4_3/bn_1/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.796565: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_0/gamma not found in checkpoint
2018-06-07 16:49:03.797159: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_1/MSkNet_WT32/block4_3/bn_1/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.797825: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_2/prelu_acti_0/alpha not found in checkpo                  int
2018-06-07 16:49:03.799135: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_1/MSkNet_WT32/block4_3/bn_1/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.800353: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_1/MSkNet_WT32/block4_3/bn_1/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.801403: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_0/moving_variance not found in check                  point
2018-06-07 16:49:03.800536: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_1/beta not found in checkpoint
2018-06-07 16:49:03.803186: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_0/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.804242: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_1/moving_variance not found in check                  point
2018-06-07 16:49:03.804466: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/conv_0/w not found in checkpoint
2018-06-07 16:49:03.807948: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_1/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.809318: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/prelu_acti_0/alpha not found in checkpo                  int
2018-06-07 16:49:03.810782: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/prelu_acti_1/alpha not found in checkpo                  int
2018-06-07 16:49:03.811674: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/bn_1/gamma not found in checkpoint
2018-06-07 16:49:03.810922: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block4_3/conv_1/w not found in checkpoint
2018-06-07 16:49:03.811958: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_0/gamma not found in checkpoint
2018-06-07 16:49:03.813234: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample1_bn_prelu/bn_/MSkNet_WT32/downsample1                  _bn_prelu/bn_/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.813488: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample1_bn_prelu/bn_/MSkNet_WT32/downsample1                  _bn_prelu/bn_/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.814435: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample1_bn_prelu/bn_/beta not found in check                  point
2018-06-07 16:49:03.817865: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_0/beta not found in checkpoint
2018-06-07 16:49:03.819454: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample1_bn_prelu/prelu_acti_/alpha not found                   in checkpoint
2018-06-07 16:49:03.818536: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample1_bn_prelu/bn_/MSkNet_WT32/downsample1                  _bn_prelu/bn_/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.818337: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample1_bn_prelu/bn_/MSkNet_WT32/downsample1                  _bn_prelu/bn_/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.820938: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample1_bn_prelu/bn_/moving_variance not fou                  nd in checkpoint
2018-06-07 16:49:03.822375: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample1_bn_prelu/conv_/w not found in checkp                  oint
2018-06-07 16:49:03.822849: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample1_bn_prelu/bn_/gamma not found in chec                  kpoint
2018-06-07 16:49:03.824896: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample2_bn_prelu/bn_/MSkNet_WT32/downsample2                  _bn_prelu/bn_/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.825245: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_0/MSkNet_WT32/block2_1/bn_0/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.829245: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample1_bn_prelu/bn_/moving_mean not found i                  n checkpoint
2018-06-07 16:49:03.829730: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample2_bn_prelu/bn_/MSkNet_WT32/downsample2                  _bn_prelu/bn_/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.830023: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample2_bn_prelu/bn_/beta not found in check                  point
2018-06-07 16:49:03.831599: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample2_bn_prelu/bn_/MSkNet_WT32/downsample2                  _bn_prelu/bn_/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.832419: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample2_bn_prelu/bn_/moving_mean not found i                  n checkpoint
2018-06-07 16:49:03.834817: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_0/MSkNet_WT32/block2_1/bn_0/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.835047: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample2_bn_prelu/bn_/MSkNet_WT32/downsample2                  _bn_prelu/bn_/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.835595: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample2_bn_prelu/conv_/w not found in checkp                  oint
2018-06-07 16:49:03.837626: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample2_bn_prelu/bn_/gamma not found in chec                  kpoint
2018-06-07 16:49:03.838629: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample2_bn_prelu/bn_/moving_variance not fou                  nd in checkpoint
2018-06-07 16:49:03.839984: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/final_pred/w not found in checkpoint
2018-06-07 16:49:03.840651: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse1_bn_prelu/bn_/MSkNet_WT32/fuse1_bn_prelu/bn                  _/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.841554: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse1_bn_prelu/bn_/MSkNet_WT32/fuse1_bn_prelu/bn                  _/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.846858: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/downsample2_bn_prelu/prelu_acti_/alpha not found                   in checkpoint
2018-06-07 16:49:03.848202: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse1_bn_prelu/bn_/gamma not found in checkpoint
2018-06-07 16:49:03.848759: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse1_bn_prelu/bn_/moving_mean not found in chec                  kpoint
2018-06-07 16:49:03.849212: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_0/MSkNet_WT32/block2_1/bn_0/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.849395: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse1_bn_prelu/bn_/MSkNet_WT32/fuse1_bn_prelu/bn                  _/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.851605: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse1_bn_prelu/bn_/beta not found in checkpoint
2018-06-07 16:49:03.853202: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse1_bn_prelu/bn_/moving_variance not found in                   checkpoint
2018-06-07 16:49:03.853546: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse1_bn_prelu/conv_/w not found in checkpoint
2018-06-07 16:49:03.854194: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block2_1/bn_0/MSkNet_WT32/block2_1/bn_0/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.854565: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse1_bn_prelu/prelu_acti_/alpha not found in ch                  eckpoint
2018-06-07 16:49:03.855026: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse1_bn_prelu/bn_/MSkNet_WT32/fuse1_bn_prelu/bn                  _/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.859269: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse2_bn_prelu/bn_/MSkNet_WT32/fuse2_bn_prelu/bn                  _/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.859519: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse2_bn_prelu/bn_/MSkNet_WT32/fuse2_bn_prelu/bn                  _/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.859780: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/prelu_acti_1/alpha not found in checkpo                  int
2018-06-07 16:49:03.859889: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse2_bn_prelu/bn_/gamma not found in checkpoint
2018-06-07 16:49:03.861195: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse2_bn_prelu/bn_/beta not found in checkpoint
2018-06-07 16:49:03.862586: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse2_bn_prelu/bn_/MSkNet_WT32/fuse2_bn_prelu/bn                  _/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.868109: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse2_bn_prelu/bn_/moving_mean not found in chec                  kpoint
2018-06-07 16:49:03.869362: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse3_bn_prelu/bn_/MSkNet_WT32/fuse3_bn_prelu/bn                  _/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.872838: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse2_bn_prelu/prelu_acti_/alpha not found in ch                  eckpoint
2018-06-07 16:49:03.873376: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse2_bn_prelu/conv_/w not found in checkpoint
2018-06-07 16:49:03.873668: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse3_bn_prelu/bn_/MSkNet_WT32/fuse3_bn_prelu/bn                  _/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.873958: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse3_bn_prelu/bn_/MSkNet_WT32/fuse3_bn_prelu/bn                  _/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.874252: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/prelu_acti_0/alpha not found in checkpo                  int
2018-06-07 16:49:03.874985: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse2_bn_prelu/bn_/MSkNet_WT32/fuse2_bn_prelu/bn                  _/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.875380: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse2_bn_prelu/bn_/moving_variance not found in                   checkpoint
2018-06-07 16:49:03.880100: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/conv_1/w not found in checkpoint
2018-06-07 16:49:03.878646: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse3_bn_prelu/bn_/beta not found in checkpoint
2018-06-07 16:49:03.878427: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse3_bn_prelu/bn_/gamma not found in checkpoint
2018-06-07 16:49:03.886963: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse3_bn_prelu/prelu_acti_/alpha not found in ch                  eckpoint
2018-06-07 16:49:03.888211: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse3_bn_prelu/bn_/moving_variance not found in                   checkpoint
2018-06-07 16:49:03.888403: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse4_bn_prelu/bn_/MSkNet_WT32/fuse4_bn_prelu/bn                  _/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.888903: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/conv_0/w not found in checkpoint
2018-06-07 16:49:03.890341: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse3_bn_prelu/conv_/w not found in checkpoint
2018-06-07 16:49:03.891088: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse3_bn_prelu/bn_/moving_mean not found in chec                  kpoint
2018-06-07 16:49:03.891237: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse3_bn_prelu/bn_/MSkNet_WT32/fuse3_bn_prelu/bn                  _/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.892414: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse4_bn_prelu/bn_/MSkNet_WT32/fuse4_bn_prelu/bn                  _/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.894474: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse4_bn_prelu/bn_/MSkNet_WT32/fuse4_bn_prelu/bn                  _/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.894907: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse4_bn_prelu/bn_/beta not found in checkpoint
2018-06-07 16:49:03.896740: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse4_bn_prelu/bn_/MSkNet_WT32/fuse4_bn_prelu/bn                  _/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.896890: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_1/moving_variance not found in check                  point
2018-06-07 16:49:03.897931: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse4_bn_prelu/bn_/gamma not found in checkpoint
2018-06-07 16:49:03.900650: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse4_bn_prelu/bn_/moving_mean not found in chec                  kpoint
2018-06-07 16:49:03.905050: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse4_bn_prelu/bn_/moving_variance not found in                   checkpoint
2018-06-07 16:49:03.908066: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse4_bn_prelu/conv_/w not found in checkpoint
2018-06-07 16:49:03.909956: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/fuse4_bn_prelu/prelu_acti_/alpha not found in ch                  eckpoint
2018-06-07 16:49:03.919520: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up1_bn_prelu/bn_/MSkNet_WT32/pred_up1_bn_pr                  elu/bn_/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.919767: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up1_bn_prelu/bn_/moving_mean not found in c                  heckpoint
2018-06-07 16:49:03.920006: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up1_bn_prelu/bn_/MSkNet_WT32/pred_up1_bn_pr                  elu/bn_/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.922563: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up1_bn_prelu/bn_/gamma not found in checkpo                  int
2018-06-07 16:49:03.922811: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up1_bn_prelu/bn_/beta not found in checkpoi                  nt
2018-06-07 16:49:03.923132: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up1_bn_prelu/bn_/MSkNet_WT32/pred_up1_bn_pr                  elu/bn_/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.923409: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_1/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.924250: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up1_bn_prelu/bn_/moving_variance not found                   in checkpoint
2018-06-07 16:49:03.930495: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_1/gamma not found in checkpoint
2018-06-07 16:49:03.931610: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_1_bn_prelu/bn_/MSkNet_WT32/pred_up2_1_b                  n_prelu/bn_/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.932086: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up1_bn_prelu/deconv_/w not found in checkpo                  int
2018-06-07 16:49:03.933208: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_1_bn_prelu/bn_/MSkNet_WT32/pred_up2_1_b                  n_prelu/bn_/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.933760: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up1_bn_prelu/prelu_acti_/alpha not found in                   checkpoint
2018-06-07 16:49:03.933578: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_1_bn_prelu/bn_/MSkNet_WT32/pred_up2_1_b                  n_prelu/bn_/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.936595: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up1_bn_prelu/bn_/MSkNet_WT32/pred_up1_bn_pr                  elu/bn_/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.938355: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_1_bn_prelu/bn_/gamma not found in check                  point
2018-06-07 16:49:03.938978: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_1_bn_prelu/bn_/moving_variance not foun                  d in checkpoint
2018-06-07 16:49:03.942008: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_1_bn_prelu/bn_/moving_mean not found in                   checkpoint
2018-06-07 16:49:03.942900: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_1_bn_prelu/bn_/MSkNet_WT32/pred_up2_1_b                  n_prelu/bn_/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.943240: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_1/beta not found in checkpoint
2018-06-07 16:49:03.943870: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_1_bn_prelu/bn_/beta not found in checkp                  oint
2018-06-07 16:49:03.945721: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_2_bn_prelu/bn_/MSkNet_WT32/pred_up2_2_b                  n_prelu/bn_/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.944674: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_1_bn_prelu/prelu_acti_/alpha not found                   in checkpoint
2018-06-07 16:49:03.948531: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_1_bn_prelu/deconv_/w not found in check                  point
2018-06-07 16:49:03.948751: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_1/MSkNet_WT32/block1_2/bn_1/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.949282: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_2_bn_prelu/bn_/beta not found in checkp                  oint
2018-06-07 16:49:03.949327: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_2_bn_prelu/bn_/MSkNet_WT32/pred_up2_2_b                  n_prelu/bn_/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.950561: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_2_bn_prelu/bn_/MSkNet_WT32/pred_up2_2_b                  n_prelu/bn_/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.950939: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_2_bn_prelu/bn_/moving_mean not found in                   checkpoint
2018-06-07 16:49:03.951062: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_2_bn_prelu/bn_/gamma not found in check                  point
2018-06-07 16:49:03.951641: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_2_bn_prelu/bn_/moving_variance not foun                  d in checkpoint
2018-06-07 16:49:03.952870: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_2_bn_prelu/bn_/MSkNet_WT32/pred_up2_2_b                  n_prelu/bn_/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.953408: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_1/MSkNet_WT32/block1_2/bn_1/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.957825: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_2_bn_prelu/prelu_acti_/alpha not found                   in checkpoint
2018-06-07 16:49:03.960666: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up2_2_bn_prelu/deconv_/w not found in check                  point
2018-06-07 16:49:03.961732: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_1_bn_prelu/bn_/MSkNet_WT32/pred_up3_1_b                  n_prelu/bn_/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.962243: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_1/MSkNet_WT32/block1_2/bn_1/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.963563: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_1_bn_prelu/bn_/MSkNet_WT32/pred_up3_1_b                  n_prelu/bn_/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.963626: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_1_bn_prelu/bn_/MSkNet_WT32/pred_up3_1_b                  n_prelu/bn_/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.966159: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_1_bn_prelu/bn_/gamma not found in check                  point
2018-06-07 16:49:03.966792: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_1_bn_prelu/bn_/moving_mean not found in                   checkpoint
2018-06-07 16:49:03.967785: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_1_bn_prelu/deconv_/w not found in check                  point
2018-06-07 16:49:03.968538: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_1_bn_prelu/prelu_acti_/alpha not found                   in checkpoint
2018-06-07 16:49:03.967346: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_1_bn_prelu/bn_/MSkNet_WT32/pred_up3_1_b                  n_prelu/bn_/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.968817: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_1_bn_prelu/bn_/beta not found in checkp                  oint
2018-06-07 16:49:03.969277: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_2_bn_prelu/bn_/MSkNet_WT32/pred_up3_2_b                  n_prelu/bn_/moving_mean/biased not found in checkpoint
2018-06-07 16:49:03.972586: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_2_bn_prelu/bn_/MSkNet_WT32/pred_up3_2_b                  n_prelu/bn_/moving_variance/local_step not found in checkpoint
2018-06-07 16:49:03.972783: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_2_bn_prelu/bn_/MSkNet_WT32/pred_up3_2_b                  n_prelu/bn_/moving_variance/biased not found in checkpoint
2018-06-07 16:49:03.973164: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_1/MSkNet_WT32/block1_2/bn_1/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.973209: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_2_bn_prelu/bn_/beta not found in checkp                  oint
2018-06-07 16:49:03.974780: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_2_bn_prelu/bn_/gamma not found in check                  point
2018-06-07 16:49:03.975008: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_2_bn_prelu/bn_/MSkNet_WT32/pred_up3_2_b                  n_prelu/bn_/moving_mean/local_step not found in checkpoint
2018-06-07 16:49:03.975206: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_1_bn_prelu/bn_/moving_variance not foun                  d in checkpoint
2018-06-07 16:49:03.982353: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_0/MSkNet_WT32/block1_1/bn_0/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.983749: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_0/MSkNet_WT32/block1_1/bn_0/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.984215: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_2_bn_prelu/bn_/moving_variance not foun                  d in checkpoint
2018-06-07 16:49:03.984049: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_2_bn_prelu/bn_/moving_mean not found in                   checkpoint
2018-06-07 16:49:03.984375: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_2_bn_prelu/prelu_acti_/alpha not found                   in checkpoint
2018-06-07 16:49:03.988183: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_0/MSkNet_WT32/block1_1/bn_0/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:03.988802: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/pred_up3_2_bn_prelu/deconv_/w not found in check                  point
2018-06-07 16:49:03.989806: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_0/moving_mean not found in checkpoin                  t
2018-06-07 16:49:03.989954: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_0/MSkNet_WT32/block1_1/bn_0/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:03.993477: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_0/moving_variance not found in check                  point
2018-06-07 16:49:03.993544: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_0/beta not found in checkpoint
2018-06-07 16:49:03.995244: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_1/MSkNet_WT32/block1_1/bn_1/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:03.995327: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_0/moving_variance not found in check                  point
2018-06-07 16:49:03.995499: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_1/MSkNet_WT32/block1_1/bn_1/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:03.995649: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_1/MSkNet_WT32/block1_1/bn_1/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:04.000388: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_0/moving_mean not found in checkpoin                  t
2018-06-07 16:49:04.003205: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_1/beta not found in checkpoint
2018-06-07 16:49:04.004334: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_1/gamma not found in checkpoint
2018-06-07 16:49:04.004093: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_1/moving_mean not found in checkpoin                  t
2018-06-07 16:49:04.005004: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_0/gamma not found in checkpoint
2018-06-07 16:49:04.005923: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/conv_0/w not found in checkpoint
2018-06-07 16:49:04.006291: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_0/gamma not found in checkpoint
2018-06-07 16:49:04.006242: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_1/moving_variance not found in check                  point
2018-06-07 16:49:04.006583: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/bn_1/MSkNet_WT32/block1_1/bn_1/moving_v                  ariance/local_step not found in checkpoint
2018-06-07 16:49:04.009295: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/conv_1/w not found in checkpoint
2018-06-07 16:49:04.009625: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/prelu_acti_0/alpha not found in checkpo                  int
2018-06-07 16:49:04.013006: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_0/MSkNet_WT32/block1_2/bn_0/moving_v                  ariance/biased not found in checkpoint
2018-06-07 16:49:04.014468: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_0/beta not found in checkpoint
2018-06-07 16:49:04.014728: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_1/prelu_acti_1/alpha not found in checkpo                  int
2018-06-07 16:49:04.014813: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_0/MSkNet_WT32/block1_2/bn_0/moving_m                  ean/biased not found in checkpoint
2018-06-07 16:49:04.015063: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_0/MSkNet_WT32/block1_2/bn_0/moving_m                  ean/local_step not found in checkpoint
2018-06-07 16:49:04.015712: W tensorflow/core/framework/op_kernel.cc:1198] Not found: Key MSkNet_WT32/block1_2/bn_0/MSkNet_WT32/block1_2/bn_0/moving_v                  ariance/local_step not found in checkpoint

incompatibility new tensorflow

Iterator is not present anymore. Fortunately, It seems it is not even used in the code. Might be possible to remove it and therefore gain compatibility with latest TF.

Duplicate entries in train_names_all_lggx3.txt

Is there a reason why the LGG dataset have multiple entries in train_names_all_lggx3.txt.

test_all_classes tests only class=2

Hello,
I have tried to test using the network but it seems from the config file test_all_classes that actually only class 2 gets predicted. could you tell me how to update that config file to test for class 1,2,3,4?

Regards,

ERROR (nifti_image_write_hdr_img2): cannot open output file

Hello Everyone,
I'm facing this error right now..

INFO:niftynet: Restoring parameters from model17/msnet_en32sg_20000.ckpt
INFO:niftynet: Restoring parameters from model17/msnet_en32cr_20000.ckpt
Data load, 100.0% finished
** ERROR (nifti_image_write_hdr_img2): cannot open output file '/result17/HGG/Brats17_CBICA_ATX_1.nii.gz'
HGG/Brats17_CBICA_ATX_1
** ERROR (nifti_image_write_hdr_img2): cannot open output file '/result17/HGG/Brats17_CBICA_AXN_1.nii.gz'
HGG/Brats17_CBICA_AXN_1
test time 124.04104340076447
Traceback (most recent call last):
File "test.py", line 460, in
test(config_file)
File "test.py", line 450, in test
np.savetxt(save_folder + '/test_time.txt', test_time)
File "/home/zaaba/anaconda3/lib/python3.6/site-packages/numpy/lib/npyio.py", line 1307, in savetxt
open(fname, 'wt').close()
FileNotFoundError: [Errno 2] No such file or directory: '/result17/test_time.txt'

Sorry if this error is a newbie mistake... :(

Test - ERROR: cannot open output file

@taigw When I run following command
python test.py config17/test_all_class.txt

I face the following error:
Data load, 100.0% finished
** ERROR (nifti_image_write_hdr_img2): cannot open output file 'result17/HGG/Brats17_CBICA_ATX_1.nii.gz'
HGG/Brats17_CBICA_ATX_1
** ERROR (nifti_image_write_hdr_img2): cannot open output file 'result17/HGG/Brats17_CBICA_AXN_1.nii.gz'
HGG/Brats17_CBICA_AXN_1
test time 16.6796910763
Traceback (most recent call last):
File "test.py", line 459, in <module>
test(config_file)
File "test.py", line 449, in test
np.savetxt(save_folder + '/test_time.txt', test_time)
File "/usr/local/lib/python2.7/dist-packages/numpy/lib/npyio.py", line 1307, in savetxt
open(fname, 'wt').close()
IOError: [Errno 2] No such file or directory: 'result17/test_time.txt'

Could you please suggest the solution.

IndexError

@taigw while running the train.py I am facing the IOError. Please can you suggest the solution.

Traceback (most recent call last):

File "", line 1, in
runfile('/home/ujjwal/brats17-master/train.py', wdir='/home/ujjwal/brats17-master')

File "/home/ujjwal/anaconda2/lib/python2.7/site-packages/spyder/utils/site/sitecustomize.py", line 880, in runfile
execfile(filename, namespace)

File "/home/ujjwal/anaconda2/lib/python2.7/site-packages/spyder/utils/site/sitecustomize.py", line 94, in execfile
builtins.execfile(filename, *where)

File "/home/ujjwal/brats17-master/train.py", line 121, in
config_file = str(sys.argv[1])

IndexError: list index out of range

How to use multi-gpu?

This program seems to only run on one GPU . Can anyone tell me how to run with multiple GPUs?
I have assigned GPU 2 and 3 with instruction "export CUDA_VISIBLE_DEVICES=2,3 ".

UnboundedLocalError: local variable referenced before assignment.

Hi,

In test.py, specifically, here, I find that the variable data_shape1ax has been referenced, but if I am using the single network (i.e., if(config_net1) is True) for whole tumor (similarly for other two tumor networks) data_shape1ax (similarly for data_shape2ax and data_shape3ax) will be undefined.

I get the following error:
UnboundedLocalError: local variable 'data_shape1ax' referenced before assignment.

Question about data and label shape

@taigw in the config file, data_shape= [19, 144, 144, 4], label_shape= [11, 144, 144, 1],why the label has different shape with the data, shouldn't the label shape=[19,144,144,1] ?
Thanks for your answers

AssertionError

@taigw
I tried for the code of training i am getting the assertion error. What will be the solution for this?

Thank you.

ujjwal@ujjwal-precision-t1700:~/Desktop/ALL_TRIES/brats17-master_NIFTYNET$ python train.py config17/train_wt_ax.txt
data data_root /home/ujjwal/Desktop/ALL_TRIES/brats17-master_NIFTYNET/data_root/Brats17TrainingData /home/ujjwal/Desktop/ALL_TRIES/brats17-master_NIFTYNET/data_root/Brats17TrainingData
data data_names config17/train_names_all.txt config17/train_names_all.txt
data modality_postfix [flair, t1, t1ce, t2] ['flair', 't1', 't1ce', 't2']
data label_postfix seg seg
data file_postfix nii.gz nii.gz
data with_ground_truth True True
data batch_size 5 5
data data_shape [19, 144, 144, 4] [19, 144, 144, 4]
data label_shape [11, 144, 144, 1] [11, 144, 144, 1]
data label_convert_source [0, 1, 2, 4] [0, 1, 2, 4]
data label_convert_target [0, 1, 1, 1] [0, 1, 1, 1]
data batch_slice_direction axial axial
data train_with_roi_patch False False
data label_roi_mask None
data roi_patch_margin None
network net_type MSNet MSNet
network net_name MSNet_WT32 MSNet_WT32
network downsample_twice True True
network class_num 2 2
training learning_rate 1e-3 0.001
training decay 1e-7 1e-07
training maximal_iteration 20000 20000
training snapshot_iteration 5000 5000
training start_iteration 0 0
training test_iteration 100 100
training test_step 10 10
training model_pre_trained None
training model_save_prefix model17/msnet_wt32 model17/msnet_wt32
size of predicty: Tensor("MSNet_WT32/final_pred/conv:0", shape=(5, 11, 144, 144, 2), dtype=float32)
2018-06-05 09:23:03.159216: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use SSE4.1 instructions, but these are available on your machine and could speed up CPU computations.
2018-06-05 09:23:03.159247: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use SSE4.2 instructions, but these are available on your machine and could speed up CPU computations.
2018-06-05 09:23:03.159253: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use AVX instructions, but these are available on your machine and could speed up CPU computations.
2018-06-05 09:23:03.159256: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use AVX2 instructions, but these are available on your machine and could speed up CPU computations.
2018-06-05 09:23:03.159260: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use FMA instructions, but these are available on your machine and could speed up CPU computations.
Data load, 49.0196078431% finished
Data load, 98.0392156863% finished
Traceback (most recent call last):
File "train.py", line 124, in
train(config_file)
File "train.py", line 83, in train
dataloader.load_data()
File "/home/ujjwal/Desktop/ALL_TRIES/brats17-master_NIFTYNET/util/data_loader.py", line 91, in load_data
volume, volume_name = self.__load_one_volume(self.patient_names[i], self.modality_postfix[mod_idx])
File "/home/ujjwal/Desktop/ALL_TRIES/brats17-master_NIFTYNET/util/data_loader.py", line 69, in __load_one_volume
assert(volume_name is not None)
AssertionError

Many errors in the code - 'Iterator'/ 'regularizers' / '_logger'

Hello dear sir or madam, and thanks for the tool.

I downloaded your tool with great pleasure, but during testing, we noticed that it contains many bugs and that

AttributeError: module 'tensorflow.tools.api.generator.api.logging' has no attribute '_logger'

from tensorflow.contrib.data import Iterator
ImportError: cannot import name 'Iterator'

from tensorflow.contrib.layers.python.layers import regularizers
ImportError: cannot import name 'regularizers'

Maybe it is because of the new version of tensorflow, please can you review the code and tell us how to start it.

Thanks

AttributeError: 'tuple' object has no attribute 'shape'

I wonder why it always has this error:
AttributeError: 'tuple' object has no attribute 'shape'

flip in __get_one_batch function

@taigw What is the use of flip in __get_one_batch function of data_loader.py?

if(flip):
    sub_data_moda = np.flip(sub_data_moda, -1)

I do see that its default value is set to False. But how would the data be affected by setting it to True?

Can I stop training early?

When I run "python train config/*", how do I judge wheather its overfitting or under-fitting?

the validation data segmentation result

I have tested your given models under the model17 directory on the validation data by submitting the segmentation results to the CBICA Image Processing Portal. However, I didn't get the same result you presented in the paper. The dice values and Hausdorff values are (0.7572, 0.8989, 0.8350) and ( 3.7947, 5.7439, 7.3037) respectively, In your paper, the values are (0.7859, 0.9050, 0.8378) and (3.2821, 3.8901, 6.4790) respectively. Would you like tell me if you apply any other methods such as model ensemble to get the result in the paper?

How to enable NiftyNet's balanced window sampler?

Hi,

I have a highly imbalanced data-distributon(3-4% of total voxels represent the object of interest) for my problem. I would like to know how to enable Niftynet's balanced window sampler here? Do I need to modify the get_subimage_batch() method?

Further, would you please suggest other features of your code which can be used to address the class-imbalance problem. I am using ROI patches for training with improved results and planning to use the tversky loss function in future.

test_one_image_three_nets_adaptive_shape function

Hi,
Thank you for this code !
I am trying to reproduce this work for a vessel segmentation project without using nifty net command line and eager execution.
The training step inspired from your code worked well but I am having trouble testing it.
Where can I find the test_one_image_three_nets_adaptive_shape function mentioned in test.py ?
Has anyone found a way to test a pretrained and restored model using NiftyNet ?

Thanks for your help !

loss is not declined

hello~I'm a student in Tianjin University,recently i am trying to train the model,but i find that the loss is not declined, just between 0.15 and 0.3,so could you tell me the reason?thank you very much!

Do I have to rewrite test.py when I define the network without NiftyNet?

I didn't change test.py but the config file.
At the line 272(The third line here):
print(all_vars)
net1ax_vars = [x for x in all_vars if x.name[0:len(net_name1ax) + 1]==net_name1ax + '/']
saver1ax = tf.train.Saver(net1ax_vars)
saver1ax.restore(sess, config_net1ax['model_file'])

I got an error:
ValueError: No variables to save

I checked all_vars and I found it seems that no variable named begin with net_name1ax

I tried to make my network inherit from 'TrainableLayer' and add a line below in function init
super(MSNet, self).__init__(name=name)
But it didn't work

Do I have to rewrite the network by using NiftyNet?
Or rewrite test.py？

Some confusion about Training Model

Hello Everyone

  I want to train a model for mysef ,so I run the train.py  with 2015 Brats Data.

 However , the result of loss changes from 0.2 to 0.3 randomly.

 Thus, even I am unable to achieve convergence.

 So, I am confused that whether this is the reason for imperfectly segmentation.

Train:MemoryError occuried

My computer is:

windows 10
GTX1060 6G
16G DDR4 2400Mhz

When I run the" python train.py train_wt_ax.txt" , i meet this problem:

Traceback (most recent call last):
File "D:\TF\brats17-master\train.py", line 123, in
train(config_file)
File "D:\TF\brats17-master\train.py", line 82, in train
dataloader.load_data()
File "D:\TF\brats17-master\util\data_loader.py", line 112, in load_data
volume = itensity_normalize_one_volume(volume)
File "D:\TF\brats17-master\util\data_process.py", line 95, in itensity_normalize_one_volume
out = (volume - mean)/std
MemoryError

At the same time, I found that my memory utilization is close to 100% from the Task Manager.

Please tell me whether i can get some solutions to this problems. Any help will be appreciated sincerely!

Overlap in Train/Test Data

I noticed that numerous files overlap in your train_all/test_all config files- wondering if I'm missing something in how these configs are processed but I would think you should not train on test data...

Memory error, while training after data loading.

Are multiple GPU's supported? Getting same error with single, multiple GPU's (8gb each)

ResourceExhaustedError (see above for traceback): OOM when allocating tensor with shape[5,17,72,72,32] and type float on /job:localhost/replica:0/task:0/device:GPU:0 by allocator GPU_0_bfc
[[Node: gradients/MSNet_WT32/block2_2/prelu_acti_0/Abs_grad/Sign = SignT=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:GPU:0"]]
Hint: If you want to see a list of allocated tensors when OOM happens, add report_tensor_allocations_upon_oom to RunOptions for current allocation info.

 [[Node: gradients/loss_function/mul_6_grad/tuple/group_deps/_754 = _Recv[client_terminated=false, recv_device="/job:localhost/replica:0/task:0/device:CPU:0", send_device="/job:localhost/replica:0/task:0/device:GPU:0", send_device_incarnation=1, tensor_name="edge_4124_gradients/loss_function/mul_6_grad/tuple/group_deps", tensor_type=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:CPU:0"]()]]

About the size of data_shape

Hello, senior fellow apprentice. I have heard a lot about you！

I changed the model structure on the basis of your model, and the training process was smooth. However, a large number of problems occurred in data-shape during the test.

During the training and testing, did you follow the relevant principles in choosing the data_shape size?

No module named 'util'

unable to locate util package for evaluation.py

How to reproduce same results as the saved pretrained models.

Do we need change anything in configuration file to get same results as pretrained models?

Cannot output image

When trying to run test.py, data is loaded correctly but when it's time to output, we get this error:

** ERROR (nifti_image_write_hdr_img2): cannot open output file 'result18/HGG/Brats18_CBICA_ANP_1.nii.gz'
HGG/Brats18_CBICA_ANP_1
test time 666.759003162384

Have you ever run into this problem?

Config File Generation for brats 2018 Data

I am looking to use some of the pretrained models on 2018 data and was wondering if there was a way to procedurally generate a "config18" directory with the relevant data file calls organized in config files. I assume that you did not manually populate these files for config15 and 17.

ResourceExhaustedError (see above for traceback): OOM when allocating tensor with shape[5,19,180,160,4]

Specs:
Linux-Ubuntu 16.04
Nvidia GEForce 940 MX
2 GB graphics card

Using tensorflow-gpu to run a project in python and have imported niftynet, simpleITK

Following is the error:
ResourceExhaustedError (see above for traceback): OOM when allocating tensor with shape[5,19,180,160,4]
[[Node: MSNet_WT32_1/block1_1/bn_0/moments/SquaredDifference = SquaredDifference[T=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:GPU:0"](_arg_Placeholder_9_0_0/_5365, MSNet_WT32_1/block1_1/bn_0/moments/StopGradient)]]
[[Node: Reshape_19/_5367 = _Recvclient_terminated=false, recv_device="/job:localhost/replica:0/task:0/device:CPU:0", send_device="/job:localhost/replica:0/task:0/device:GPU:0", send_device_incarnation=1, tensor_name="edge_1584_Reshape_19", tensor_type=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:CPU:0"]]

Following is the code of test.py
test.txt

load data problem

2018-06-22 21:55:22.938552: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1030] Found device 0 with properties:
name: GeForce GTX 1080 Ti major: 6 minor: 1 memoryClockRate(GHz): 1.645
pciBusID: 0000:01:00.0
totalMemory: 10.92GiB freeMemory: 10.51GiB
2018-06-22 21:55:22.938573: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1120] Creating TensorFlow device (/device:GPU:0) -> (device: 0, name: GeForce GTX 1080 Ti, pci bus id: 0000:01:00.0, compute capability: 6.1)
Data load, 17.54385964912281% finished
Data load, 35.08771929824562% finished
Data load, 52.63157894736842% finished
killed

how much memory it needs at least to load all 100% data and run this project?

Activation Layer Before Convolution layer in ResBlock

In file MSNet.py while creating (or defining) the graph for the model, I noticed that in the function that creates a residual block the activation layer is being applied before convolution. Is that a mistake or I am missing something considering we don't apply activation before Convolution?

Some questions about data_root

Hello, thank you very much for your code. I am a beginner. I want to know what path does data_root represent if I put Brats training set into data_root? Is it the root directory of the project or the freely set directory?

Where can we find the labels for Brats 2015 dataset?

It seems we are not able to find labels for Brats 2015 dataset from the website https://www.smir.ch/BRATS/Start2015, though the download link claimed so, would you help to point us to where we can access the labels? Thank you so much!

Error: Provided indices are out-of-bounds

Hi,

I am trying to train model with brats18 data. If you could please help debugging an error.

The error generates while executing train.py file at line "dice = loss.eval(feed_dict ={x:tempx, w:tempw, y:tempy})"
During "step"=0 it works fine, and then at "step"=1, it gives error.

Below is the traceback:
(myEnv) PS C:\Users\Jayendra\Desktop\brats17-master\brats17-master> python .\train.py .\config17\train_wt_ax.txt
C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\dtypes.py:469: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_qint8 = np.dtype([("qint8", np.int8, 1)])
C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\dtypes.py:470: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_quint8 = np.dtype([("quint8", np.uint8, 1)])
C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\dtypes.py:471: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_qint16 = np.dtype([("qint16", np.int16, 1)])
C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\dtypes.py:472: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_quint16 = np.dtype([("quint16", np.uint16, 1)])
C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\dtypes.py:473: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_qint32 = np.dtype([("qint32", np.int32, 1)])
C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\dtypes.py:476: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
data data_root C:\Users\Jayendra\Desktop\brats17-master\brats17-master\data_root\Brats17TrainingData C:\Users\Jayendra\Desktop\brats17-master\brats17-master\data_root\Brats17TrainingData
data data_names config17\train_names_all.txt config17\train_names_all.txt
data modality_postfix [flair, t1, t1ce, t2] ['flair', 't1', 't1ce', 't2']
data label_postfix seg seg
data file_postfix nii.gz nii.gz
data with_ground_truth True True
data batch_size 5 5
data data_shape [19, 144, 144, 4] [19, 144, 144, 4]
data label_shape [11, 144, 144, 1] [11, 144, 144, 1]
data label_convert_source [0, 1, 2, 3] [0, 1, 2, 3]
data label_convert_target [0, 1, 1, 1] [0, 1, 1, 1]
data batch_slice_direction axial axial
data train_with_roi_patch False False
data label_roi_mask None
data roi_patch_margin None
network net_type MSNet MSNet
network net_name MSNet_WT32 MSNet_WT32
network downsample_twice True True
network class_num 2 2
training learning_rate 1e-3 0.001
training decay 1e-7 1e-07
training maximal_iteration 20000 20000
training snapshot_iteration 5000 5000
training start_iteration 0 0
training test_iteration 100 100
training test_step 10 10
training model_pre_trained None
training model_save_prefix C:\Users\Jayendra\Desktop\brats17-master\brats17-master\model17\msnet_wt32 C:\Users\Jayendra\Desktop\brats17-master\brats17-master\model17\msnet_wt32
size of predicty: Tensor("MSNet_WT32/final_pred/conv:0", shape=(5, 11, 144, 144, 2), dtype=float32)
0.001
jay_before_opt_step
name: "Adam"
op: "NoOp"
input: "^Adam/update_MSNet_WT32/block1_1/bn_0/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_1/bn_0/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_1/prelu_acti_0/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_1/conv_0/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_1/bn_1/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_1/bn_1/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_1/prelu_acti_1/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_1/conv_1/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_2/bn_0/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_2/bn_0/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_2/prelu_acti_0/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_2/conv_0/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_2/bn_1/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_2/bn_1/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_2/prelu_acti_1/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block1_2/conv_1/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse1_bn_prelu/conv/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse1_bn_prelu/bn/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse1_bn_prelu/bn/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse1_bn_prelu/prelu_acti/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/downsample1_bn_prelu/conv/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/downsample1_bn_prelu/bn_/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/downsample1_bn_prelu/bn_/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/downsample1_bn_prelu/prelu_acti_/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_1/bn_0/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_1/bn_0/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_1/prelu_acti_0/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_1/conv_0/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_1/bn_1/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_1/bn_1/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_1/prelu_acti_1/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_1/conv_1/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_2/bn_0/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_2/bn_0/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_2/prelu_acti_0/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_2/conv_0/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_2/bn_1/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_2/bn_1/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_2/prelu_acti_1/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block2_2/conv_1/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse2_bn_prelu/conv_/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse2_bn_prelu/bn_/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse2_bn_prelu/bn_/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse2_bn_prelu/prelu_acti_/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/downsample2_bn_prelu/conv_/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/downsample2_bn_prelu/bn_/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/downsample2_bn_prelu/bn_/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/downsample2_bn_prelu/prelu_acti_/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_1/bn_0/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_1/bn_0/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_1/prelu_acti_0/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_1/conv_0/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_1/bn_1/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_1/bn_1/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_1/prelu_acti_1/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_1/conv_1/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_2/bn_0/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_2/bn_0/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_2/prelu_acti_0/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_2/conv_0/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_2/bn_1/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_2/bn_1/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_2/prelu_acti_1/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_2/conv_1/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_3/bn_0/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_3/bn_0/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_3/prelu_acti_0/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_3/conv_0/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_3/bn_1/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_3/bn_1/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_3/prelu_acti_1/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block3_3/conv_1/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse3_bn_prelu/conv_/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse3_bn_prelu/bn_/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse3_bn_prelu/bn_/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse3_bn_prelu/prelu_acti_/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_1/bn_0/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_1/bn_0/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_1/prelu_acti_0/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_1/conv_0/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_1/bn_1/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_1/bn_1/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_1/prelu_acti_1/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_1/conv_1/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_2/bn_0/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_2/bn_0/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_2/prelu_acti_0/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_2/conv_0/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_2/bn_1/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_2/bn_1/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_2/prelu_acti_1/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_2/conv_1/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_3/bn_0/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_3/bn_0/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_3/prelu_acti_0/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_3/conv_0/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_3/bn_1/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_3/bn_1/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_3/prelu_acti_1/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/block4_3/conv_1/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse4_bn_prelu/conv_/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse4_bn_prelu/bn_/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse4_bn_prelu/bn_/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/fuse4_bn_prelu/prelu_acti_/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up1_bn_prelu/deconv_/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up1_bn_prelu/bn_/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up1_bn_prelu/bn_/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up1_bn_prelu/prelu_acti_/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up2_1_bn_prelu/deconv_/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up2_1_bn_prelu/bn_/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up2_1_bn_prelu/bn_/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up2_1_bn_prelu/prelu_acti_/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up2_2_bn_prelu/deconv_/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up2_2_bn_prelu/bn_/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up2_2_bn_prelu/bn_/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up2_2_bn_prelu/prelu_acti_/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up3_1_bn_prelu/deconv_/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up3_1_bn_prelu/bn_/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up3_1_bn_prelu/bn_/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up3_1_bn_prelu/prelu_acti_/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up3_2_bn_prelu/deconv_/w/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up3_2_bn_prelu/bn_/beta/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up3_2_bn_prelu/bn_/gamma/ApplyAdam"
input: "^Adam/update_MSNet_WT32/pred_up3_2_bn_prelu/prelu_acti_/alpha/ApplyAdam"
input: "^Adam/update_MSNet_WT32/final_pred/w/ApplyAdam"
input: "^Adam/Assign"
input: "^Adam/Assign_1"

jay_after_opt_step
2020-05-30 11:45:22.845647: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\platform\cpu_feature_guard.cc:137] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX AVX2
2020-05-30 11:45:23.401603: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1030] Found device 0 with properties:
name: Quadro RTX 5000 major: 7 minor: 5 memoryClockRate(GHz): 1.815
pciBusID: 0000:17:00.0
totalMemory: 16.00GiB freeMemory: 13.32GiB
2020-05-30 11:45:23.608883: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1030] Found device 1 with properties:
name: Quadro RTX 5000 major: 7 minor: 5 memoryClockRate(GHz): 1.815
pciBusID: 0000:73:00.0
totalMemory: 16.00GiB freeMemory: 13.32GiB
2020-05-30 11:45:23.801746: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1030] Found device 2 with properties:
name: Quadro RTX 5000 major: 7 minor: 5 memoryClockRate(GHz): 1.815
pciBusID: 0000:a6:00.0
totalMemory: 16.00GiB freeMemory: 13.32GiB
2020-05-30 11:45:23.821872: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1045] Device peer to peer matrix
2020-05-30 11:45:23.831541: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1051] DMA: 0 1 2
2020-05-30 11:45:23.839970: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1061] 0: Y N N
2020-05-30 11:45:23.846304: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1061] 1: N Y N
2020-05-30 11:45:23.853917: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1061] 2: N N Y
2020-05-30 11:45:23.859826: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1120] Creating TensorFlow device (/device:GPU:0) -> (device: 0, name: Quadro RTX 5000, pci bus id: 0000:17:00.0, compute capability: 7.5)
2020-05-30 11:45:23.870241: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1120] Creating TensorFlow device (/device:GPU:1) -> (device: 1, name: Quadro RTX 5000, pci bus id: 0000:73:00.0, compute capability: 7.5)
2020-05-30 11:45:23.877451: I C:\tf_jenkins\home\workspace\rel-win\M\windows-gpu\PY\36\tensorflow\core\common_runtime\gpu\gpu_device.cc:1120] Creating TensorFlow device (/device:GPU:2) -> (device: 2, name: Quadro RTX 5000, pci bus id: 0000:a6:00.0, compute capability: 7.5)
jay_before_sess
<tensorflow.python.client.session.InteractiveSession object at 0x000001CA5DB267B8>
jay_after_sess
<tensorflow.python.training.saver.Saver object at 0x000001CA5DB5FE48>
Data load, 100.0% finished
20000
5000
0
100
10
0
0
100
10
0 ("this is value of "step")
jay_after_step
0.534315 ("this is dice value for "step" 0")
1 ("this is value of "step")
Traceback (most recent call last):
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\client\session.py", line 1323, in _do_call
return fn(*args)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\client\session.py", line 1302, in _run_fn
status, run_metadata)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\errors_impl.py", line 473, in exit
c_api.TF_GetCode(self.status.status))
tensorflow.python.framework.errors_impl.InvalidArgumentError: Provided indices are out-of-bounds w.r.t. dense side with broadcasted shape
[[Node: loss_function/mul = SparseDenseCwiseMul[T=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:CPU:0"](loss_function/stack, loss_function/ones_like, loss_function/ToInt64_2, loss_function/Softmax)]]

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File ".\train.py", line 144, in
train(config_file)
File ".\train.py", line 123, in train
dice = loss.eval(feed_dict ={x:tempx, w:tempw, y:tempy})
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\ops.py", line 570, in eval
return _eval_using_default_session(self, feed_dict, self.graph, session)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\ops.py", line 4455, in _eval_using_default_session
return session.run(tensors, feed_dict)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\client\session.py", line 889, in run
run_metadata_ptr)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\client\session.py", line 1120, in _run
feed_dict_tensor, options, run_metadata)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\client\session.py", line 1317, in _do_run
options, run_metadata)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\client\session.py", line 1336, in _do_call
raise type(e)(node_def, op, message)
tensorflow.python.framework.errors_impl.InvalidArgumentError: Provided indices are out-of-bounds w.r.t. dense side with broadcasted shape
[[Node: loss_function/mul = SparseDenseCwiseMul[T=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:CPU:0"](loss_function/stack, loss_function/ones_like, loss_function/ToInt64_2, loss_function/Softmax)]]

Caused by op 'loss_function/mul', defined at:
File ".\train.py", line 144, in
train(config_file)
File ".\train.py", line 71, in train
loss = loss_func(predicty, y, weight_map = w)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\niftynet\layer\base_layer.py", line 32, in call
return self._op(*args, **kwargs)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\ops\template.py", line 268, in call
result = self._call_func(args, kwargs, check_for_new_variables=False)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\ops\template.py", line 217, in _call_func
result = self._func(*args, **kwargs)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\niftynet\layer\loss_segmentation.py", line 61, in layer_op
pred, ground_truth, weight_map))
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\niftynet\layer\loss_segmentation.py", line 320, in dice
one_hot * prediction, reduction_axes=[0])
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\ops\math_ops.py", line 905, in binary_op_wrapper_sparse
name=name), sp_x.dense_shape)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\ops\gen_sparse_ops.py", line 851, in sparse_dense_cwise_mul
sp_shape=sp_shape, dense=dense, name=name)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\op_def_library.py", line 787, in _apply_op_helper
op_def=op_def)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\ops.py", line 2956, in create_op
op_def=op_def)
File "C:\Users\Jayendra\anaconda3\envs\myEnv\lib\site-packages\tensorflow\python\framework\ops.py", line 1470, in init
self._traceback = self._graph._extract_stack() # pylint: disable=protected-access

InvalidArgumentError (see above for traceback): Provided indices are out-of-bounds w.r.t. dense side with broadcasted shape
[[Node: loss_function/mul = SparseDenseCwiseMul[T=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:CPU:0"](loss_function/stack, loss_function/ones_like, loss_function/ToInt64_2, loss_function/Softmax)]]

(myEnv) PS C:\Users\Jayendra\Desktop\brats17-master\brats17-master>

OOM about training with brats17 data

hello, I have some problem about this code, please help me.
I use the GPU: v100 16G.
but when I try to train the net with brats17 data by your code, I get OOM. I only used 70% data of brats17.
from the code, It looks like it load all the data into it.
I hope to know some about dataloading when your training with brats17.

net1 output is null

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