Advancing 3D Medical Image Analysis with Variable Dimension Transform based Supervised 3D Pre-training
This is an implementation of our paper Advancing 3D Medical Image Analysis with Variable Dimension Transform based Supervised 3D Pre-training.
Modified from mmclassification.
Support 3D ResNet pre-training with 2D natural-image dataset.
Please refer to install.md for installation.
Download ImageNet dataset and put it as the following structure:
data
├──imagenet
├── get_meta.sh
├── meta
│ ├── val.txt
│ ├── test.txt
│ ├── train.txt
├── val
│ ├──ILSVRC2012_val_00000001.JPEG
│ ├──ILSVRC2012_val_00000002.JPEG
│ ├── ...
├── test
│ ├──ILSVRC2012_test_00000001.JPEG
│ ├──ILSVRC2012_test_00000002.JPEG
│ ├── ...
└── train
└── n10148035
│ ├── n10148035_10034.JPEG
│ ├── n10148035_10371.JPEG
│ ├── ...
└── n11879895
│ ├── ...
└── ...
Run this script to pre-train a 3D-ResNet-18 model on ImageNet dataset. It will take around 7 days on 8 Titan XP GPUs.
bash pre_train.sh
We provide models pre-trained on ImageNet dataset which can be used for different 3D medical image analysis tasks.
The pre-trained 3D-ResNet-18 model can be downloaded from BaiduYun(verification code: 865y) or GoogleDrive.
We also provide pretrained models of other compared methods for convenience, which can be avaliable at BaiduYun(verification code: 1ezg) or GoogleDrive. Note that the first convolution layer of some pretrained models are with input channels of 3(same as imagenet pretrained models), which is inconsistent with 1-channel CT slice input. To fully use the pretrained weights, we averaged the parameters of the first conv layer so that it can take 1-channel input data. These models are end with suffixes like _med1channel.pth
.
LIDC-Classification
Data split can be found in data/lidc.
bash tools/dist_train.sh configs/LIDC_Cls_configs/resnet18_3d_BN_b32x4_LIDC_cos_smoo.py $NUM_GPUS
Data split can be found in medseg/data.
We provide a implementation modified from mmsegmentation for segmentation experiments on BCV, LIDC and LiTS datasets. Please run corresponding bash files under medseg
folder.
medseg/bcv_test.sh
medseg/bcv_train.sh
medseg/lidc_test.sh
medseg/lidc_train.sh
medseg/LiTS_test.sh
medseg/LiTS_train.sh
Please refer to our another repo to run experiments on the DeepLesion dataset. To train a P3D63 model, run:
bash tools/dist_train.sh configs/deeplesion/p3d.py 8
If you have questions or suggestions, please open an issue here.