arnab39 / fewshot_gan-unet3d Goto Github PK

I got the following error when running python main_unset.py --training

2019-09-12 21:17:30.594167: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2019-09-12 21:17:31.140393: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1405] Found device 0 with properties: 
name: GeForce RTX 2080 Ti major: 7 minor: 5 memoryClockRate(GHz): 1.545
pciBusID: 0000:1a:00.0
totalMemory: 10.73GiB freeMemory: 10.57GiB
2019-09-12 21:17:31.324298: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1405] Found device 1 with properties: 
name: GeForce RTX 2080 Ti major: 7 minor: 5 memoryClockRate(GHz): 1.545
pciBusID: 0000:1b:00.0
totalMemory: 10.73GiB freeMemory: 10.57GiB
2019-09-12 21:17:31.508353: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1405] Found device 2 with properties: 
name: GeForce RTX 2080 Ti major: 7 minor: 5 memoryClockRate(GHz): 1.545
pciBusID: 0000:3d:00.0
totalMemory: 10.73GiB freeMemory: 10.57GiB
2019-09-12 21:17:31.691047: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1405] Found device 3 with properties: 
name: GeForce RTX 2080 Ti major: 7 minor: 5 memoryClockRate(GHz): 1.545
pciBusID: 0000:3e:00.0
totalMemory: 10.73GiB freeMemory: 10.57GiB
2019-09-12 21:17:31.691543: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1484] Adding visible gpu devices: 0, 1, 2, 3
2019-09-12 21:17:33.385536: I tensorflow/core/common_runtime/gpu/gpu_device.cc:965] Device interconnect StreamExecutor with strength 1 edge matrix:
2019-09-12 21:17:33.385595: I tensorflow/core/common_runtime/gpu/gpu_device.cc:971]      0 1 2 3 
2019-09-12 21:17:33.385603: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] 0:   N N N N 
2019-09-12 21:17:33.385608: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] 1:   N N N N 
2019-09-12 21:17:33.385613: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] 2:   N N N N 
2019-09-12 21:17:33.385618: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] 3:   N N N N 
2019-09-12 21:17:33.386348: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 10439 MB memory) -> physical GPU (device: 0, name: GeForce RTX 2080 Ti, pci bus id: 0000:1a:00.0, compute capability: 7.5)
2019-09-12 21:17:33.589232: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:1 with 10439 MB memory) -> physical GPU (device: 1, name: GeForce RTX 2080 Ti, pci bus id: 0000:1b:00.0, compute capability: 7.5)
2019-09-12 21:17:33.799606: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:2 with 10439 MB memory) -> physical GPU (device: 2, name: GeForce RTX 2080 Ti, pci bus id: 0000:3d:00.0, compute capability: 7.5)
2019-09-12 21:17:33.995857: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:3 with 10439 MB memory) -> physical GPU (device: 3, name: GeForce RTX 2080 Ti, pci bus id: 0000:3e:00.0, compute capability: 7.5)
2019-09-12 21:18:10.689782: E tensorflow/stream_executor/cuda/cuda_dnn.cc:352] Could not create cudnn handle: CUDNN_STATUS_INTERNAL_ERROR
Fatal Python error: Segmentation fault

Thread 0x00007f1e85266740 (most recent call first):
  File "/home/skyuuka/anaconda2/envs/FewShot_GAN-Unet3D/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 1350 in _call_tf_sessionrun
  File "/home/skyuuka/anaconda2/envs/FewShot_GAN-Unet3D/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 1263 in _run_fn
  File "/home/skyuuka/anaconda2/envs/FewShot_GAN-Unet3D/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 1278 in _do_call
  File "/home/skyuuka/anaconda2/envs/FewShot_GAN-Unet3D/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 1272 in _do_run
  File "/home/skyuuka/anaconda2/envs/FewShot_GAN-Unet3D/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 1100 in _run
  File "/home/skyuuka/anaconda2/envs/FewShot_GAN-Unet3D/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 877 in run
  File "/home/skyuuka/anaconda2/envs/FewShot_GAN-Unet3D/lib/python3.5/site-packages/tensorflow/python/framework/ops.py", line 4986 in _run_using_default_session
  File "/home/skyuuka/anaconda2/envs/FewShot_GAN-Unet3D/lib/python3.5/site-packages/tensorflow/python/framework/ops.py", line 2241 in run
  File "/home/skyuuka/workspace/FewShot_GAN-Unet3D/unet3D/model_unet.py", line 213 in train
  File "main_unet.py", line 62 in main
  File "/home/skyuuka/anaconda2/envs/FewShot_GAN-Unet3D/lib/python3.5/site-packages/tensorflow/python/platform/app.py", line 125 in run
  File "main_unet.py", line 69 in <module>

Error message:
\FewShot_GAN-Unet3D-master\pytorch\graphs\models\custom_functions\weight_norm.py",
line 165, in forward
output_padding = self._output_padding(input, output_size, self.stride, self.padding,
self.kernel_size)
TypeError: _output_padding() missing 1 required positional argument: 'num_spatial_dims'

It states that the num_spatial_dims argument is missing from line 165 in the weight_norm python file (within the 'forward' definition). What should this value for nums_spatial_dims be? Thank you!

$python main.py configs/unet.json
The error was happended.
What should you do?

I tried to train and test unet3D with
"epoch", 90
"number_train_images", 5
but the output of CSF,GM,WM are all 0 (I have already checked the input image and label, Label unique:[0 10 150 250])

I also train and test proposed_model and the output image is as follows

Ask for help！Thanks a lot！

Did you try replacing U-Net with a new upgraded U-Net version called Isensee Model+3DGAN? How do you think the results may vary?

how to train on my own dataset?

File "C:\Users\virkt\Anaconda3\envs\unet\lib\multiprocessing\reduction.py", line 244
def init(dump)
^
SyntaxError: invalid syntax

OSError: No command "N4BiasFieldCorrection" found on host tx-eva-stianci. Please check that the corresponding package is installed.

CUDA error: device-side assert triggered

The iseg2017 data is used, and the data format is hdr. The loss here is a tensor, and no value is returned. How to solve this problem?
run FewShot_GAN-Unet3D-master/pytorch/agents/supervised_baseline.py

self.criterion =nn.CrossEntropyLoss(class_weights)
loss = self.criterion(output_logits, labels)
loss.backward()
self.optimizer.step()

hi,
I recently downloaded data. it does not contain .nii files. In preprocess.py I changed
to pattern = '{0}/{1}/{3}/subject-{2}-{3}.img'
from pattern = '{0}/{1}/{3}/subject-{2}-{3}.nii'

But later on I gain get error during unet training .
ImageFileError: Cannot work out file type of "../data/iSEG_preprocessed/Training/label/subject-1-label.img"
How to solve the issue from the beginning! or what else I can do further?
Thanks

Your approach is interesting. Please consider having it incorporated into the following toolkits if you haven't already:

https://github.com/NifTK/NiftyNet
https://github.com/perone/medicaltorch
https://github.com/pfjaeger/medicaldetectiontoolkit

Doing this can dramatically increase the audience of your approach. Thanks.

I am getting error . What can be the problem here.

`Training
1
../data/iSEG_preprocessed/Training/T1/subject-1-T1.nii
../data/iSEG_preprocessed/Training/T2/subject-1-T2.nii
../data/iSEG_preprocessed/Training/label/subject-1-label.nii
Extracting Patches from Image 1 ....
Total Extracted Labelled Patches Shape: (2605, 32, 32, 32, 2) (2605, 32, 32, 32)
../data/iSEG_preprocessed/Testing/T1/subject-11-T1.nii
../data/iSEG_preprocessed/Testing/T2/subject-11-T2.nii
../data/iSEG_preprocessed/Training/label/subject-1-label.nii
Processing the Image 11 ....
Traceback (most recent call last):
File "main.py", line 81, in
tf.app.run()
File "/home/hmahmood/anaconda3/envs/pi352/lib/python3.5/site-packages/tensorflow/python/platform/app.py", line 126, in run
_sys.exit(main(argv))
File "main.py", line 73, in main
network.train()
File "/home/hmahmood/FewShot_GAN-Unet3D/proposed_model/model.py", line 223, in train
data_directory=F.data_directory)
File "../preprocess/preprocess.py", line 311, in init
patch_shape, number_unlab_images_training)

File "../preprocess/preprocess.py", line 246, in preprocess_dynamic_unlab
x=get_patches_unlab(T1_vols, T2_vols, extraction_step, patch_shape,dir)
File "../preprocess/preprocess.py", line 205, in get_patches_unlab
label_patches = extract_patches(label_ref, patch_shape, extraction_step)
File "../preprocess/preprocess.py", line 81, in extract_patches
dstride_d:(dstride_d)+patch_d]
ValueError: could not broadcast input array from shape (32,32,32,1) into shape (32,32,32)`

我想问一下那个model_unet.py函数中259行的那个recompose3D_overlap函数是怎么定义的，源程序好像没有定义，请教大神，我的邮箱是[email protected]，QQ号是2919028238

I am new to medical imaging. I get this output outputimage_unet_4.nii.gz
how to analyze this?
and how to display in similar as you are showing.
Thanks

Dear Arnab,

It's not clear for me how did you choose the class weights? Did you estimate weights similar to compute_class_weight only from the training data? Did you fine-tune the weights manually?

Background- 0.33, CSF- 1.5, GM- 0.83, WM- 1.33: https://github.com/arnab39/FewShot_GAN-Unet3D/blob/master/unet3D/model_unet.py#L152.

btw Thanks a lot for sharing your code and paper. Sadly, there was nothing said about class weights in your paper.

Best regards,
Stas

Hi, I have covert .img to .nii, but when i run python main.py(bad gan), the error is
File "E:/slycode\FewShot_GAN-Unet3D-master\preprocess\preprocess.py", line 305, in init
patch_shape,number_images_training)
File "E:/slycode\FewShot_GAN-Unet3D-master\preprocess\preprocess.py", line 162, in preprocess_dynamic_lab
T1_vols[(case_idx-c-1), :, :, :] = read_vol(case_idx, 'T1', dir)
ValueError: could not broadcast input array from shape (144,192,256,1) into shape (144,192,256)
should i change the (144,192,256) in the preprocess.py to (144,192,256,1)???

I get the loss of the validation:17.218517 for the first time ,but afterwards it doesn't change even a little,I completely follow the instructions of the program . Is it the problem that I ignore some details or the program get some little problem with the model ?