mt-diff

Processing of dual encoded magnetization and diffusion data, from pre-processsing to connectomes. Manuscript available on arxiv:https://arxiv.org/abs/2303.03449

Acquisition

This analysis requires data from a custom dual-encoded magnetization-transfer and diffusion-weigthed sequence (Leppert et al. ,ISMRM 2022, Abstract #1044). Available for Siemens software version VE11c. The pipeline expects consists of 2 datasets, one with and one without MT saturation.

Dependencies

• MRTrix3 https://www.mrtrix.org/
• MRtrix3Tissue https://3tissue.github.io/
• afni https://afni.nimh.nih.gov/
• ANTs https://github.com/ANTsX/ANTs/wiki/ANTS-and-antsRegistration
• FreeSurfer https://github.com/freesurfer/freesurfer
• FSL https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation
• COMMIT https://github.com/daducci/COMMIT

Pipeline

Setup

Setup paths and dependencies

init.sh

Preprocessing

• Anatomical segmentation with FreeSurfer
• Eddy current and distortion correction, as well and B1 bias correction of the diffusion

aa2_preprocesssing_samebias.sh

Diffusion processing

• Compute fiber orientation distribution function
• Tractography
• Connectome

bb1_Script_05_iPOF_ss3t_tractography_upsampling_as_ISMRM.sh

COMMIT processing

• Generate confidence map

cc1_condfidence_map.sh

• Setup environment

dd1_enable_python_venv.sh

• Apply COMMIT on MTon and MToff datasets

dd2_COMMIT_MToff_as_ISMRM.py

dd3_COMMIT_MTon_as_ISMRM.py

• Apply COMMIT results to MToff and MTon connectomes and compute MTR

ee1_connectomes_MToff_jointFilter.py

ee2_connectomes_MTon_jointFilter.py

ff1_MTRconnectome.py

• Map COMMIT results back onto tracts

gg1_MTR_bundle.py

gg2_MTRdw_bundle.py

Data availability

Sample data is available through Dataverse (https://doi.org/10.5683/SP3/LNFHGO) or upon request through a formal data sharing agreement and approval from the local ethics committees.

The dataset contains the dual-encoded raw MT-weighted diffusion data and processed files for 1 subject. It also contains the MTR connectivity matrices (tract-specific and tractometry) for all 10 subjects (scan-rescan)