ihMT pipeline

===================

Flow to process ihMT images. This flow generated four myelin indices maps from the inhomogeneous Magnetization Transfer (ihMT) images.

Input Data recommendation:

• it is recommended to use dcm2niix (v1.0.20200331) to convert data https://github.com/rordenlab/dcm2niix/releases/tag/v1.0.20200331
• dcm2niix conversion will create all echo files for each contrast and corresponding json files
• all input must have a matching json file with the same filename
• all contrasts must have a same number of echoes and coregistered between them before running the script.
• Mask must be coregistered to the echo images
• ANTs can be used for the registration steps (http://stnava.github.io/ANTs/)

A full description is available in this reference: https://onlinelibrary.wiley.com/doi/10.1002/hbm.26310. The supplementary data provide the ihMT maps computations in more detail.

Requirements

• Nextflow
• scilpy
• ants

Singularity

If you are on Linux, we recommend using the Singularity container to run ihMT_flow

Prebuild Singularity images are available here:

https://scil.usherbrooke.ca/pages/containers/

FOR DEVELOPERS: The containers repository is available here: containers-scilus

Steps

• Coregistration of images (ANTs)
• Brain extraction (FSL bet)
• Segmentation (ANTs)
• Compute ihMT maps (Scilpy)
• Registration to diffusion space using Register T1 of Tractoflow (ANTs)

Output

• ihMT dR1 saturation (ihMTsat)
• ihMT ratio (ihMTR)
• MT saturation (MTsat)
• MT Ratio (MTR)

Myelin-sensitive maps in native space: Contrasts_ihMT_maps and ihMT_native_maps folders.

Myelin-sensitive maps in diffusion space: Register_contrast_maps and Register_ihMT_maps folders.

** Update for PK (main_pk_analysis.nf): Include Contrast maps in Diffusion space as output.

Usage

See USAGE or run nextflow run main.nf --help

References

Varma G, Girard OM, Prevost VH, Grant AK, Duhamel G, Alsop DC.
Interpretation of magnetization transfer from inhomogeneously broadened lines
(ihMT) in tissues as a dipolar order effect within motion restricted molecules.
Journal of Magnetic Resonance. 1 nov 2015;260:67-76.

Manning AP, Chang KL, MacKay AL, Michal CA. The physical mechanism of
"inhomogeneous" magnetization transfer MRI. Journal of Magnetic Resonance.
1 janv 2017;274:125-36.

Helms G, Dathe H, Kallenberg K, Dechent P. High-resolution maps of
magnetization transfer with inherent correction for RF inhomogeneity
and T1 relaxation obtained from 3D FLASH MRI. Magnetic Resonance in Medicine.
2008;60(6):1396-407.
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