MRtoUS

Generate US images from MR brain images.

Setup

Following steps only apply if you want to create pre-processed dataset from scratch otherwise download this.

1. Download the group2 dataset.
2. Download and install the minc toolset.

Registration

Uses ground truth landmarks to align US and MR volumes.

# export the register transformation in the GUI
register -sync 01_mr_tal.mnc 01a_us_tal.mnc 01_all.tag

# apply the transformation to ultrasound images
mincresample 01a_us_tal.mnc 01_us_reg.mnc -transformation 01_reg.xfm -like 01_mr_tal.mnc

Conversion

The MNI-BITE dataset uses MINC-1.0 and MINC-2.0 format. Later extends HDF5 which has a maintained python implementation h5py.

mincconvert -2 01_mr_tal.mnc 01_mr.mnc

Dependencies

Install python dependencies.

pip3 install -r requirements.txt