Computational protocol: White matter predicts functional connectivity in premanifest Huntington's disease

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Protocol publication

[…] Initial preprocessing steps were performed using FSL. For the diffusion data the b = 0 image was used to generate a brain mask using FSL's brain extraction tool. Eddy current correction was used to align the diffusion‐weighted volumes to the first b = 0 image and the gradient directions updated to reflect the changes to the image orientations. Finally, diffusion tensor metrics were calculated and constrained spherical deconvolution (CSD) applied to the data as implemented in MRtrix. Freesufer ROIs were warped into diffusion space by mapping between the T1‐weighted image and fractional anisotropy (FA) map using NiftyReg and applying the resulting warp to each of the ROIs. A foreground mask was generated by combining Freesurfer segmentations with the WM mask. A summary of the processing pipeline is provided in Figure . [...] Whole brain probabilistic tractography was performed using the iFOD2 algorithm in MRtrix. Specifically, 5 million streamlines were seeded throughout the WM, in all foreground voxels where FA > 0.2. Streamlines were terminated when they either reached the cortical or subcortical gray‐matter mask or exited the foreground mask. The spherical deconvolution informed filtering of tractograms (SIFT) algorithm was used to reduce biases. The resulting set of streamlines was used to construct the structural brain network. […]

Pipeline specifications

Software tools BET, SIFT
Applications Magnetic resonance imaging, Diffusion magnetic resonance imaging analysis
Organisms Homo sapiens
Diseases Huntington Disease, Neurodegenerative Diseases