Comments (7)
To save memeory, the training and testing were based on image patches, not the entire image size. The convolution in the z-axis was based on 'valid' mode, that's why the output size is reduced by 8 in z-axis.
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That is so wired!
I use the dataset of BRATS15, the original data shape is 155 * 240 * 240, but the sub image shape is 19 * 144 * 144.
According to his function ,
center_point = get_random_roi_sampling_center(volume_shape, sub_label_shape, batch_sample_model, boundingbox) #
and also
sub_data_moda = extract_roi_from_volume(transposed_volumes[moda],center_point,sub_data_shape)
it seems that your randomly get a sub image by cropping the original image, which I think may miss some information of the tumor.
How do you guarantee this cropping method will get all the tumor information we want?
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I love this question, I run the MSNet and get 91.4% in whole tumor segmentation on BRATS2015 with this (19, 144, 144, 4), but I don't understand why 19 and 11.
from brats17.
I love this question, I run the MSNet and get 91.4% in whole tumor segmentation on BRATS2015 with this (19, 144, 144, 4), but I don't understand why 19 and 11.
Well, it is the problem of the model if self !
You could revise util/MSNet.py like
if __name__ == '__main__':
x = tf.placeholder(tf.float32, shape = [1, 96, 96, 96, 1])
y = tf.placeholder(tf.float32, shape = [1, 96, 96, 96, 2])
net = MSNet(num_classes=2)
predicty = net(x, is_training = True)
print(x)
print(predicty)
print (Y)
ant run it like
python util/MSNet.py
You will find that the result is
shape .....
(1, 96, 96, 96, 1)
(1, 88, 96, 96, 2)
(1, 96, 96, 96, 2)
I hope this could help you solve the problem
from brats17.
I love this question, I run the MSNet and get 91.4% in whole tumor segmentation on BRATS2015 with this (19, 144, 144, 4), but I don't understand why 19 and 11.
Well, it is the problem of the model if self !
You could revise util/MSNet.py likeif __name__ == '__main__': x = tf.placeholder(tf.float32, shape = [1, 96, 96, 96, 1]) y = tf.placeholder(tf.float32, shape = [1, 96, 96, 96, 2]) net = MSNet(num_classes=2) predicty = net(x, is_training = True) print(x) print(predicty) print (Y)
ant run it like
python util/MSNet.py
You will find that the result is
shape ..... (1, 96, 96, 96, 1) (1, 88, 96, 96, 2) (1, 96, 96, 96, 2)
I hope this could help you solve the problem
我又思考了一遍,沿着axial轴截了19(155),但是后续沿着coronal, sagittal方向,也是截了19,三个长方体叠起来,是不是覆盖了大部分范围。
from brats17.
I love this question, I run the MSNet and get 91.4% in whole tumor segmentation on BRATS2015 with this (19, 144, 144, 4), but I don't understand why 19 and 11.
Well, it is the problem of the model if self !
You could revise util/MSNet.py likeif __name__ == '__main__': x = tf.placeholder(tf.float32, shape = [1, 96, 96, 96, 1]) y = tf.placeholder(tf.float32, shape = [1, 96, 96, 96, 2]) net = MSNet(num_classes=2) predicty = net(x, is_training = True) print(x) print(predicty) print (Y)
ant run it like
python util/MSNet.py
You will find that the result isshape ..... (1, 96, 96, 96, 1) (1, 88, 96, 96, 2) (1, 96, 96, 96, 2)
I hope this could help you solve the problem
我又思考了一遍,沿着axial轴截了19(155),但是后续沿着coronal, sagittal方向,也是截了19,三个长方体叠起来,是不是覆盖了大部分范围。
yeah! As you know, the shape of raw data is 155 * 240 * 240, but we only randomly select some data with shape of 19 * 144 * 144 from the raw data. This is because with a large iteration (like here is 20000), we can cover the whole data (155 * 240 * 240)probabilistically speaking.
I guess he did so because it could help save the memory use when training or testing!
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Related Issues (20)
- ERROR (nifti_image_write_hdr_img2): cannot open output file HOT 11
- the validation data segmentation result HOT 3
- How to use multi-gpu? HOT 1
- Do I have to rewrite test.py when I define the network without NiftyNet? HOT 1
- About the size of data_shape HOT 9
- UnboundedLocalError: local variable referenced before assignment.
- Activation Layer Before Convolution layer in ResBlock HOT 1
- net1 output is null HOT 2
- Can I stop training early?
- Some questions about data_root
- test_one_image_three_nets_adaptive_shape function
- Config File Generation for brats 2018 Data
- Overlap in Train/Test Data
- How to enable NiftyNet's balanced window sampler?
- loss is not declined HOT 1
- OOM about training with brats17 data HOT 1
- Error: Provided indices are out-of-bounds
- No module named 'util'
- Where can we find the labels for Brats 2015 dataset?
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