Read and validate a diffusion MRI gradient table.

The main entry point for reading diffusion gradients. It reads b-vectors and b-values from either a pair of FSL-style files or from a single MRtrix-style gradient table file, checks that they are consistent, and reports suspicious entries. Use this rather than calling read.dti.bvec and read.dti.bval separately if you intend to use the gradients for anything, because a mismatched or malformed gradient table is silently wrong otherwise.

Usage

read.dti.gradients(bvec, bval = NULL, n_volumes = NULL, layout = "auto")

Arguments

bvec

character string (path to a b-vectors file), or a numeric matrix with one row per volume (or one column per volume) and 3 columns.

bval

character string (path to a b-values file), or a numeric vector with one value per volume. Can be NULL if bvec identifies both files.

n_volumes

scalar numeric or integer, the number of volumes in the DWI image that the gradients belong to, used to check that the table matches the image. Typically dim(volume$data)[4]. Set to NULL (the default) to skip this check.

layout

character string, passed on to the readers, one of 'auto', 'components' or 'volumes'.

Value

a named list with the entries bvec (numeric matrix with n rows and 3 columns, one row per volume, components in image space) and bval (numeric vector of length n).

Details

Both parameters accept either a file path or already read data, so the function can also be used to validate gradients that were obtained from somewhere else. If bval is NULL and bvec is a single file path, the file is interpreted as follows. A file whose name contains bvec is read as a b-vectors file (since the name is the user's clearest statement about the content, and a b-vectors file with 4 volumes would otherwise look exactly like a 3-volume gradient table). Otherwise, a file that has 4 values per line, or 4 lines, is read as an MRtrix gradient table. Otherwise the file is read as b-vectors and a matching b-values file is looked up next to it, which covers the common dataset layouts such as BIDS (sub-01_dwi.bvec with sub-01_dwi.bval).

Note

The following problematic cases are reported, but the data is always returned as read, except for the missing values, which are replaced by zeros: (1) NA/NaN entries, which are interpreted as b=0 volumes, as MRtrix3 does, provided that they do not leave a volume with a b-value but no direction or vice versa, which is an error; (2) gradient vectors whose norm deviates from 1, which is reported because MRtrix3 rescales the b-value by the squared norm in this situation; (3) volumes with a b-value above the b=0 threshold but a zero direction; (4) volumes with a small positive b-value but a non-zero direction.

See also

Other dti functions: read.dti.bval(), read.dti.bvec(), read.dti.grad(), write.dti.bval(), write.dti.bvec(), write.dti.grad()