README.md

Medial Tractography Analysis (MeTA)

MeTA is a workflow implemented to minimize microstructural heterogeneity in diffusion MRI (dMRI) metrics by extracting and parcellating the core volume along the bundle length in the voxel-space directly while effectively preserving bundle shape and efficiently capturing the regional variation within and along white matter (WM) bundles.

Contact: Iyad Ba Gari [email protected]

If you use MeTA code, please cite the following publication:

• Heritability and Genetic Correlations Along the Corticospinal Tract. In International Workshop on Computational Diffusion MRI, CDMRI 2024 (Accepted)
• Ba Gari, I., et al.: Medial tractography analysis (MeTA) for white matter population analyses across datasets. In: 2023 11th International IEEE/EMBS Conference on Neural Engineering (NER). pp. 1–5 (Apr 2023)
• Ba Gari, I., et al.: Along-tract parameterization of white matter microstructure using medial tractography analysis (MeTA). In: The 19th International Symposium on Medical Information Processing and Analysis (2023)
• Yushkevich, P.A.: Continuous medial representation of brain structures using the biharmonic PDE. Neuroimage 45(1 Suppl), S99–110 (Mar 2009)

Installation

There are two options to use the package: via Conda or Docker/Singularity.

Conda Installation

Create an environment with Python version >=3.9 and <3.12. For example:

conda config --add channels bioconda
conda create -n meta python==3.10
conda install bioconda::meta-neuro

NOTE: Use meta --help to see the package options.

Docker/Singularity Installation

To pull the Singularity image:

singularity pull docker://quay.io/biocontainers/meta-neuro:1.0.0--py310haf7471d_0
singularity pull docker://quay.io/biocontainers/meta-neuro:1.0.0--py311h1752f0f_0
singularity pull docker://quay.io/biocontainers/meta-neuro:1.0.0--py39hc022aa2_0

To execute the package with Singularity:

singularity exec meta-neuro_1.0.0--py310haf7471d_0.sif meta --help

How to use the package:

• Convert streamlines in TRK format to a binary image:

meta_bundle_density --bundle CST.trk --reference dti_FA.nii.gz --output CST.nii.gz

• Generate a 3D Medial Surface for WM Bundle Using the CMREP Method:

vtklevelset CST.nii.gz CST.vtk 0.1
cmrep_vskel -c 3 -p 1.5 -g CST.vtk CST_skeleton.vtk

• Run Medial Tractography Analysis (MeTA):

meta --subject 1234 --bundle CST --medial_surface CST_skeleton.vtk --volume CST.vtk --sbundle CST.trk --mbundle CST_model.trk --mask CST.nii.gz --num_segments 15 --output CST

• Extract Segment Features:

meta_segment_features --subject 1234 --bundle CST --mask CST_segments_local_core.nii.gz --map FA.nii.gz --output CST_FA_15_segments_local_core_metrics.csv

• Extract Streamline Features:

meta_streamlines_features --subject 1234 --bundle CST --mask CST.nii.gz --tractogram CST.trk --output CST_streamlines_metrics.csv