lsoustelle / ihmt_proc

Minimal requirement:

• ANTs (https://github.com/ANTsX/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS)
• Bash > 4.0 (tested on Bash 4.4 & 5.0)

Additional features & dependencies:

• ihMT-MoCo [1] cannot be included in this repository since under license. The script is freely available, provided that the End User License Agreement is signed, at: https://crmbm.univ-amu.fr/ihmt-moco/

  • ihMT-MoCo requires the BET tool from FSL

• DICOMs handling: dcm2niix package & set in the PATH variable

• Degibbsing:

1. unring: mrdegibbs through MRtrix3
2. cosine apodization (python3 with nibabel & numpy): provided apodize_cos.py script

• Denoising: MP-PCA: dwidenoise through MRtrix3

• ihMTsat computation:

  • ihMTsat computation [2] is made possible (fit_ihMTsat_CLI.py), providing pre-processed ihMT and co-registered T1 map as minimal image inputs.
  • See -h option for further description about inputs/outputs.
  • The script requires up-to-date Python (developed on 3.8.2) with numpy (≥ 1.19.4), scipy (≥ 1.5.4) and nibabel (≥ 3.2.0) packages.

• References:

[1] L. Soustelle et al., A Motion Correction Strategy for Multi-Contrast based 3D parametric imaging : Application to Inhomogeneous Magnetization Transfer (ihMT), bioRxiv 2020

[2] F. Munsch et al., Characterization of the cortical myeloarchitecture with inhomogeneous magnetization transfer imaging (ihMT), NeuroImage 2020;225:117442

[3] L. Soustelle et al., A strategy to reduce the sensitivity of inhomogeneous magnetization transfer (ihMT) imaging to radiofrequency transmit field variations at 3 T, Magnetic Resonance in Medicine, 2022 (DOI: 10.1002/mrm.29055)