t2mapping

ITK-based T2 mapping

description

This project uses ITK-based T2 mapping code from:

Bigler, D., M. Meadowcroft, X. Sun, J. Vesek, A. Dresner, M. Smith, and Q. Yang. “MR Parameter Map Suite: ITK Classes for Calculating Magnetic Resonance T2 and T1 Parameter Maps,” Insight Journal, 237, 2008.

available here

and makes available an executable that takes image-TE_time pairs and performs T2 mapping.

usage

./t2mapping output_base_name algorithm threshold image1 TE1[ms] image2 TE2[ms] image3 TE3[ms] etc.

algorithm:

• 0: LINEAR least-squares fit of log(S) = log(A) - 1/T2
• 1: NON_LINEAR least-squares fit of S = A * exp(-t/T2)
• 2: NON_LINEAR_WITH_CONSTANT least-squares fit S = A* exp(-t/T2) + C

Note: you need at least 2 images for 0 and 1, at least 3 images for 2

threshold:

• Sets voxels below this threshold to 0 in all images -> no T2 calculation performed on these voxels.
• Use threshold = 3 * noise
• Use threshold=0 if you do not want thresholding

Outputs produced:

• *_t2.mha: 3D image with voxel values equal T2 [ms]
• *_A.mha: 3D image with voxel values equal to magnitude A
• *_C.mha: 3D image with voxel values equal to constant C
• *_R2.mha: 3D image with voxel values equal to r-squared of curve fit

Example: ./t2mapping result 0 90.0 image1.mha 12.0 image2.mha 56.0 image3.mha 92.0

build instructions

mkdir build
cd build
cmake ..
make

dependency

Tested with InsightToolkit-4.8.2 (ITK) and CMake 3.8.2 on MacOSx ElCapitan

license

BSD 3-Clause License (see LICENSE)