multiSliceAlignedSENSE

Tools for aligned reconstruction of multi-shot multi-slice MR.

This repository provides tools to implement the reconstruction methods and reproduce the experiments included in Figures 3 and 4 of the manuscript ''3D motion corrected SENSE reconstruction for multi-shot multi-slice MRI: application to neonatal brain imaging'', L. Cordero-Grande, E. J. Hughes, J. Hutter, A. N. Price, and J. V. Hajnal. Unpublished.

The code has been developed in MATLAB and has the following structure:

./

contains the scripts for running the experiments included in Figures 4 and 3 of the manuscript, respectively: multiSliceAlignedSENSE_Exp[1-2].m.

./lib

contains a package used to save the resulting reconstructions as nifti files: NIfTI_20140122.

./meth

contains the solvers for motion and reconstruction as well as the alternating method described in the manuscript: solve[X,T]MS2D.m, optimizeLevelMS2D.m.

./meth/pro

contains functions used by the solvers: fftGPU.m, ifftGPU.m, sense.m, isense.m, precomputeFactors3DTransform.m, transform3DSinc.m, transform3DSinc[Gradient,Hessian].m, filtering.m, mirroring.m, resampling.m, computeROI.m, extractROI.m, extractSlabs.m, sliceProfile.m.

./meth/pos

contains functions for postprocessing: gibbsRingingFilter.m, rotateMPS.m, writeNIFTI.m.

NOTE 1: Exemplary data is provided in files yT[1-2]Comp.mat, respectively for Figures 3 and 4. To run the code the user is expected to create a folder

./data

where these datasets should be located. Data generated when running the scripts is also stored in this folder.

NOTE 2: When running the scripts, set the gpu variable to 0 if your system does not support NVIDIA GPU computing under MATLAB.

NOTE 3: Computation times on an 8(16) x Intel(R) Core(TM) i7-5960X CPU @ 3.00GHz 64GB RAM with a GeForce GTX TITAN X have been:

• Figure 4 / Exp 1:
  • Conventional uncorrected SENSE reconstruction: 6".
  • Uncorrected reconstruction with slice profile filter: 16".
  • Corrected reconstruction without outlier rejection: 17'57".
  • Corrected reconstruction without within-plane motion: 19'34".
  • Corrected reconstruction without through-plane motion: 13'8".
  • Fully corrected reconstruction: 15'3".
• Figure 3 / Exp 2:
  • Conventional uncorrected SENSE reconstruction: 5".
  • Uncorrected reconstruction with slice profile filter: 22".
  • Corrected reconstruction without outlier rejection: 167'57".
  • Corrected reconstruction without within-plane motion: 24'40".
  • Corrected reconstruction without through-plane motion: 20'21".
  • Fully corrected reconstruction: 104'30".