sergivalverde / cnn-ms-lesion-segmentation

MS lesion segmentation using cascaded 3D convolutional neural networks

Hi there 👋

I'm Sergi Valverde, PhD, MBA.

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cnn-ms-lesion-segmentation's Issues

FileNotFoundError ,How i get it *.nii.gz?

---> cnn1 loading training data
Traceback (most recent call last):
File "train_leave_one_out.py", line 79, in
model = train_cascaded_model(model, train_x_data, train_y_data, options)
File "C:\Users\MAGARA\Downloads\Compressed\cnn-ms-lesion-segmentation-master\base.py", line 35, in train_cascaded_model
X, Y = load_training_data(train_x_data, train_y_data, options)
File "C:\Users\MAGARA\Downloads\Compressed\cnn-ms-lesion-segmentation-master\base.py", line 134, in load_training_data
x_patches, y_patches = load_train_patches(x_data, y_data, selected_voxels, options['patch_size'])
File "C:\Users\MAGARA\Downloads\Compressed\cnn-ms-lesion-segmentation-master\base.py", line 205, in load_train_patches
lesion_masks = [load_nii(name).get_data().astype(dtype=np.bool) for name in y_data]
File "C:\Users\MAGARA\Anaconda2\lib\site-packages\nibabel\loadsave.py", line 40, in load
raise FileNotFoundError("No such file: '%s'" % filename)
nibabel.py3k.FileNotFoundError: No such file: 'C:\Users\MAGARA\Downloads\Compressed\cnn-ms-lesion-segmentation-master\VH_all\im3\lesion_bin.nii.gz'

MemoryError

Dear professor:
I use your kears "cnn-ms-lesion-sg", my computer :NVIDIA-GT1070 8GB ,32GB RAM, cpu i7 6700.
In test, I use 5 group images as train and 5 group images as test. When epoch finish than DEBUG will memoryerror, I don't why ,can you help me ? thanks

requirements.txt errors

Hello,

I was not able to simply run pip install on the requirements file because some versions were not found. Maybe they have been updated or changed and thus not available anymore?

I have now latest version for Lasagne, etc. However, as you may expect, some issues come out. It says that theano.sandobox... gives error. I'm not really capable to find out where and what to change to make it work. Any idea what to do? Thank you very much in advance.

MemoryError

Dear professor:
I use your kears "cnn-ms-lesion-sg", my computer :NVIDIA-GT1070 8GB ,32GB RAM, cpu i7 6700.
In test, I use 5 group images as train and 5 group images as test. When epoch finish than DEBUG will memoryerror, I don't why ,can you help me ? thanks

I have a problem with filetypes

Hi @sergivalverde

I want to get data to use to run the program. I use data from MICCAI2008 (filetype *.nhdr). But the filetype does not match the specified code (filetype *.nii.gz). Where can I get it?
If you know, please answer me.

Thank you

Test

config.py

Hello Sergi,

could you please confirm us the parameters setting (e.g. modalities, epochs, batch size,...) to reproduce the MICCAI 2016 data challenge results (15 patients)? We are using the keras version of your method.

Many thanks!

I can't get a good result

Dear professor, when I use CHB and UNC data training , I can't get a good result .
about data pre-processing , I use BET skull-stripped ,but no N3 intensity normalized and smoothing ,also no resampled to 256256256 , then i train it , so because pre-processing and other?
Can you give me a suggestion.

pickle isse - NameError: global name 'pickle' is not defined

Hi,
anyone ended up with a problem of this sort - NameError: global name 'pickle' is not defined
See below for details:

model = train_cascaded_model(model, train_x_data, train_y_data, options)
File "/udd/fgalassi/base.py", line 38, in train_cascaded_model
model[0].fit(X, Y)
File "/udd/fgalassi/myenv/lib/python2.7/site-packages/nolearn/lasagne/base.py", line 700, in fit
self.train_loop(X, y, epochs=epochs)
File "/udd/fgalassi/myenv/lib/python2.7/site-packages/nolearn/lasagne/base.py", line 839, in train_loop
func(self, self.train_history_)
File "/udd/fgalassi/myenv/lib/python2.7/site-packages/nolearn_utils/hooks.py", line 60, in call
pickle.dump(train_history, f, -1)
NameError: global name 'pickle' is not defined

Thank you!

program

Dear Dr. Sergi Valverde, I download your program, my environment is ubuntu 16.04, but I use jupyter notebook cell example_1.pynb always error. I also install requirements.txt , can your help me. Thank you very much.

What is necessary steps in pre-processing data?