fedi_dmri_recon

Synopsis

Continuous and analytical diffusion signal reconstruction with 3D-SHORE.

Usage

fedi_dmri_recon [-h] -d <file> -a <file> -e <file> -u <file> -s <file>
                [-m <file>] [-do_not_use_mask] [-w <file>]

Options

Help

  • -h, –help Show this help message and exit

Mandatory

  • -d, –dmri <file> Path to the input dMRI file

  • -a, –bval <file> Path to the bval file

  • -e, –bvec_in <file> Path to the input bvec file

  • -u, –bvec_out <file> Path to the output bvec file

  • -s, –fspred <file> Path to save the reconstructed dMRI file

Optional

  • -m, –mask <file> Path to the mask file to reduce computation time

  • -do_not_use_mask Flag to indicate not to use the mask, even if provided

  • -w, –weights <file> Path to the weights file (TXT format)

References

Snoussi, Haykel, Davood Karimi, Onur Afacan, Mustafa Utkur, and Ali Gholipour. HAITCH: A framework for distortion and motion correction in fetal multi-shell diffusion-weighted MRI. Imaging Neuroscience 2025.