Is there a Convolutional Neural Network implementation for 3D images?

I'm looking for an implementation matlab, in order to process 3D CT scan images. By 3D I mean 3 spatial dimensions (i.e. not 2D+channels or 2D+time). Any advice? preferrably an accelerated version (that used GPU or mex files) and an easy-to-use pre-trained network like Elektronn but for MATLAB..

another side question: does Caffe support 3D images? if so, how can it be used through MATLAB ?

Answer 1

[Erik]

You can attempt to do a 3D CNN by the Tri-Planar approach from "Deep Feature Learning for Knee Cartilage Segmentation Using a Triplanar Convolutional Neural Network" by Prasoon et al. 2013 MICCAI. https://link.springer.com/chapter/10.1007/978-3-642-40763-5_31

Basically, instead of making a 3D window/patch around the region of interest, you use the three 2D planes. This is similar to how a radiologist will inspect the data.

Answer 2

[Joss Knight]

There are many 3D image processing algorithms in MATLAB. However, there is currently no support for 3D volumetric data in the Deep Learning framework, other than by treating each slice as an independent image. You could try MatConvNet, or perhaps give us more information about what you are trying to do, since Neural Nets are not always the answer!

[sally]

thanx alot for the reply..

I'm trying to find a classification algorithm to detect whether a 3D structure is a nodule or not, in lung CT scan.. the input would be a 3D box and can't be treated as separate images in order not to ignore the 3d features of a lung nodule..

standard algorithms could be used like support vector machines or classification trees, but I was interested in state-of-the-art algorithms to finish my thesis..

I found a MATLAB interface for the Caffe CNN, trying to use it but still having some problems running it

[Joss Knight]

I'll admit I don't have a good answer to that, other than the same basic searches that you will be doing. I would still recommend MatConvNet for an immediate way to get hold of 3D image classification networks.

Answer 3

[Muhammad]

Hi, May be it can be helpful for you. https://www.mathworks.com/matlabcentral/fileexchange/58447-hagaygarty-mdcnn?s_tid=answers_rc2-1_p4_MLT

Answer 4

[Rahul Sharma]

aNY IDEA WHICH PRETRAINED NETWORK I CAN USE FOR .NII nifti IMAGES in MATLAB