FISSILE

Fiber segmentation by signal splitting and iterative least squares estimation (FISSILE) is a method for unmixing crossing white matter fibers in diffusion MRI data.

Usage

FISSILE operates on a fiber orientation distribution (FODs) as its input. We suggest fitting using MRtrix3 with order 6 or order 8 spherical harmonics. The input should be a .mat file containing signal, a N_voxels x N_sh matrix of spherical harmonics coefficients. We suggest normalizing the FODs so that the first value is 1/sqrt(4*pi) so the FOD integrates to 1 over the surface of the sphere.

The main code is in fissile.m:

function fissile(input_file, output_file, fracFitErrorThresh, eta2, max_fibers, n_jobs)
    ...
end

• fracFitErrorThresh: The threshold for the fractional fit error (5e-2).
• eta2: The weight of the axial symmetry constraint (5).
• max_fibers: The maximum number of fibers to be segmented (10).
• n_jobs: The number of parallel jobs to be used (10).

You could run this with something like this in bash:

matlab -batch "fissile('test_input.mat', 'test_output.mat', 5e-2, 5, 10, 10)"

The output file should contain data, a MATLAB struct with the following fields:

• total_fod: the original FODs
• separate_fod: the separated FODs in fiber frames (i.e., aligned with the z-axis)
• est_theta: estimated theta value in radians for each fiber
• est_phi: estimated phi value in radians for each fiber
• est_v: estimated v value for each fiber
• rotate_separate_fod: the rotated separated FODs in lab frame

Containerized version

There is also a containerized version. See INSTALL.md for building instructions.

Run with:

docker run --rm -it -v "$(pwd)/data:/data" fissile:v1.1.3 /data/test_input.mat /data/test_output.mat 5e-2 5 10 10

Or as a singularity, available here for download:

apptainer run -e --contain -B "$(pwd)/data:/data" fissile_v1.1.3.sif /data/test_input.mat /data/test_output.mat 5e-2 5 10 10

Citation

Adam M. Saunders, Gaurav Rudravaram, Michael E. Kim, Elyssa M. McMaster, Yifan Shuai, Warren Boschen, Sophie Lin, Suzana Herculano-Houzel, Daniel C. Colvin, Yurui Gao, Kurt G. Schilling, Adam W. Anderson, and Bennett Landman. "Separating mixtures of single-fiber orientation distributions for increased sensitivity to crossing white matter fibers.” https://arxiv.org/abs/2610.20974.