MaCRUISE

Consistent cortical reconstruction and multi-atlas brain segmentation

BSD 3-Clause License

MaCRUISE is the multi-atlas predecessor of SLANT and UNesT; it pairs multi-atlas segmentation with cortical surface reconstruction.

MaCRUISE segments a T1 MRI scan to 133 labels while simultaneously reconstructing consistent cortical surfaces. The whole workflow ships as a single Docker image (about 10 GB) and runs in two steps: SLANT whole brain segmentation, followed by MaCRUISE surface reconstruction.

Usage

# Get the MaCRUISE docker image
sudo docker pull masidocker/spiders:MaCRUISE_v3_1_0

# Step 1: run SLANT whole brain segmentation
sudo nvidia-docker run -it --rm \
    -v $SLANT_input_dir:/INPUTS/ \
    -v $SLANT_output_dir:/OUTPUTS \
    masidocker/spiders:deep_brain_seg_v1_0_0 \
    /extra/run_deep_brain_seg.sh

# Step 2: run MaCRUISE surface reconstruction
sudo docker run --rm \
    -v $MaCRUISE_input_dir:/INPUTS/ \
    -v $MaCRUISE_output_dir:/OUTPUTS/ \
    masidocker/spiders:MaCRUISE_v3_1_0 \
    xvfb-run -a --server-args="-screen 0 1920x1200x24 -ac +extension GLX" \
    /extra/MaCRUISE_v3_1_0

Copy the T1 image to MaCRUISE_input_dir/T1.nii.gz and the SLANT segmentation to MaCRUISE_input_dir/orig_target_seg.nii.gz before step 2. The final refined segmentation is in MaCRUISE/Output/SegRefine, the surfaces in MaCRUISE/Output/Surfaces, and an overlay PDF in MaCRUISE/Output/PDF. The code and Docker are free for noncommercial purposes; see the repository for the commercial terms.

Yuankai Huo, Andrew J. Plassard, Aaron Carass, Susan M. Resnick, Dzung L. Pham, Jerry L. Prince, and Bennett A. Landman. “Consistent cortical reconstruction and multi-atlas brain segmentation” NeuroImage, 138 (2016): 197-210.

Yuankai Huo, Aaron Carass, Susan M. Resnick, Dzung L. Pham, Jerry L. Prince, and Bennett A. Landman. “Combining multi-atlas segmentation with brain surface estimation” In Medical Imaging 2016: Image Processing, vol. 9784, p. 97840E. International Society for Optics and Photonics, 2016.