arnab39 / fewshot_gan-unet3d Goto Github PK

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)`

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

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

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!

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

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.

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)???

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?

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()

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 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！

how to train on my own dataset?

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>

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

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 ?

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

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