文件列表:

LICENSE.md (35147, 2018-09-16)
data (0, 2018-09-16)
data\atlas_norm.npz (55052832, 2018-09-16)
data\labels.mat (432, 2018-09-16)
data\test_seg.npz (427552, 2018-09-16)
data\test_vol.npz (3189161, 2018-09-16)
ext (0, 2018-09-16)
ext\medipy-lib (0, 2018-09-16)
ext\medipy-lib\medipy (0, 2018-09-16)
ext\medipy-lib\medipy\__init__.py (21, 2018-09-16)
ext\medipy-lib\medipy\__init__.pyc (167, 2018-09-16)
ext\medipy-lib\medipy\__pycache__ (0, 2018-09-16)
ext\medipy-lib\medipy\__pycache__\__init__.cpython-35.pyc (155, 2018-09-16)
ext\medipy-lib\medipy\__pycache__\__init__.cpython-36.pyc (144, 2018-09-16)
ext\medipy-lib\medipy\__pycache__\metrics.cpython-35.pyc (1677, 2018-09-16)
ext\medipy-lib\medipy\__pycache__\metrics.cpython-36.pyc (1582, 2018-09-16)
ext\medipy-lib\medipy\metrics.py (1570, 2018-09-16)
ext\medipy-lib\medipy\metrics.pyc (1806, 2018-09-16)
ext\neuron (0, 2018-09-16)
ext\neuron\neuron (0, 2018-09-16)
ext\neuron\neuron\__init__.py (212, 2018-09-16)
ext\neuron\neuron\__pycache__ (0, 2018-09-16)
ext\neuron\neuron\__pycache__\__init__.cpython-35.pyc (462, 2018-09-16)
ext\neuron\neuron\__pycache__\callbacks.cpython-35.pyc (20049, 2018-09-16)
ext\neuron\neuron\__pycache__\dataproc.cpython-35.pyc (10632, 2018-09-16)
ext\neuron\neuron\__pycache__\generators.cpython-35.pyc (29985, 2018-09-16)
ext\neuron\neuron\__pycache__\inits.cpython-35.pyc (767, 2018-09-16)
ext\neuron\neuron\__pycache__\layers.cpython-35.pyc (19230, 2018-09-16)
ext\neuron\neuron\__pycache__\metrics.cpython-35.pyc (13157, 2018-09-16)
ext\neuron\neuron\__pycache__\models.cpython-35.pyc (20346, 2018-09-16)
ext\neuron\neuron\__pycache__\plot.cpython-35.pyc (2364, 2018-09-16)
ext\neuron\neuron\__pycache__\utils.cpython-35.pyc (33730, 2018-09-16)
ext\neuron\neuron\callbacks.py (25839, 2018-09-16)
ext\neuron\neuron\dataproc.py (14522, 2018-09-16)
ext\neuron\neuron\generators.py (52103, 2018-09-16)
ext\neuron\neuron\inits.py (603, 2018-09-16)
... ...

# voxelmorph Unsupervised Learning with CNNs for Image Registration We incorporate several variants, presented at CVPR2018 (initial unsupervised learning) and MICCAI2018 (probabilistic & diffeomorphic) ## Instructions It might be useful to have each folder inside the `ext` folder on your python path. assuming voxelmorph is setup at `/path/to/voxelmorph/`: ``` export PYTHONPATH=$PYTHONPATH:/path/to/voxelmorph/ext/neuron/:/path/to/voxelmorph/ext/pynd-lib/:/path/to/voxelmorph/ext/pytools-lib/ ``` ### Training: These instructions are for the MICCAI2018 paper. If you'd like the CVPR version (no diffeomorphism or uncertainty measures and using CC) use train.py 1. Change the top parameters in `train_miccai2018.py` to the location of your image files. 2. Run `train_miccai2018.py` with options described in the main function. Example: ``` train_miccai2018.py --gpu 0 --model_dir /my/path/to/models ``` ### Testing (measuring Dice scores): 1. Put test filenames in data/test_examples.txt, and anatomical labels in data/test_labels.mat. 2. Run `test_miccai2018.py` [gpu-id] [model_dir] [iter-num] ## Notes - We provide A T1 atlas used in our papers at data/atlas_norm.npz. - The spatial transform code, found at [`neuron.layers.SpatialTransform`](https://github.com/adalca/neuron/blob/master/neuron/layers.py), accepts N-dimensional affine and dense transforms, including linear and nearest neighbor interpolation options. Note that original development of VoxelMorph used `xy` indexing, whereas we are not emphasizing `ij` indexing. - For the MICCAI2018 version, we integrate the velocity field using [`neuron.layers.VecInt`]((https://github.com/adalca/neuron/blob/master/neuron/layers.py)). By default we integrate using scaling and squaring, which we found efficient. - You will likely need to write some of the data loading code in 'datagenerator.py' for your own datasets and data formats. There are several hard-coded elements related to data preprocessing and format. ## Papers **Unsupervised Learning for Fast Probabilistic Diffeomorphic Registration** [Adrian V. Dalca](http://adalca.mit.edu), [Guha Balakrishnan](http://people.csail.mit.edu/balakg/), [John Guttag](https://people.csail.mit.edu/guttag/), [Mert R. Sabuncu](http://sabuncu.engineering.cornell.edu/) MICCAI 2018. [eprint arXiv:1805.04605](https://arxiv.org/abs/1805.04605) **An Unsupervised Learning Model for Deformable Medical Image Registration** [Guha Balakrishnan](http://people.csail.mit.edu/balakg/), [Amy Zhao](http://people.csail.mit.edu/xamyzhao/), [Mert R. Sabuncu](http://sabuncu.engineering.cornell.edu/), [John Guttag](https://people.csail.mit.edu/guttag/), [Adrian V. Dalca](http://adalca.mit.edu) CVPR 2018. [eprint arXiv:1802.02604](https://arxiv.org/abs/1802.02604) ## Contact: For and problems or questions please open an issue in github or email us at voxelmorph@mit.edu

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