Single diffusion series:
The diffusion and anatomical datasets were registered using a mutual information based algorithm
[Maes et al., 1997] to remove image misregistration from echo planar induced image shifts and motion,
assuming that no motion occurred within a set. The diffusion directions were corrected accordingly.
If multi-run acquisitions:
Each run was linearly registered to the first diffusion series using the b=0 image, while assuming that
no motion occurred within a set. The first diffusion and anatomical datasets were then registered using a
mutual information based algorithm [Maes et al., 1997] to remove image misregistration from echo planar induced
image shifts and motion. The diffusion datasets were then transformed using the combined transformation and
concatenated rather than averaged, since the gain in SNR is equivalent and it enables the corrections to
the gradient table needed following image transformation.
- If multi-fibre reconstruction using spherical deconvolution was used:
From the diffusion weighted images, the fibre orientation distribution function (fibre ODF)
was calculated using spherical deconvolution [Anderson 2005].
- If tensor fit was used (single fibre):
A least squares diffusion tensor fit was [also] performed in order to generate fractional anisotropy
and mean diffusivity maps.
- If using FACT algorithm:
Streamline tractography was performed by following the prinicipal eigenvector direction (FACT), as described
by [Mori et al., 1999]
*describe regions of interest (ROIs)...
*if -brute-force option used:
*if -brute-force option not used:Tracking was initiated in all voxels in the volume and tracts that passed through the tract-delineating ROIs were retained.
*Below, <> signifies an input option specific to your study. If there is a default, it is here:Tracking was initiated in all voxels in the
(and tracts that passed through all of the tract-delineating ROIs were retained)
*if -exclude option used, describe those ROIs too.The tracking was initiated on a <3x3x3> grid of start points in order to facilitate branching. The tracking was stopped if the fractional anisotropy (FA) was less than <>, the mean diffusivity was greater than <>mm^2/ms, or the curvature from one voxel to the next was greater than <>^degrees.
Tracts that _______ were excluded.