# fixelreorient¶

## Synopsis¶

Reorient fixel directions

## Usage¶

fixelreorient [ options ]  fixel_in warp fixel_out

• fixel_in: the input fixel directory
• warp: a 4D deformation field used to perform reorientation. Reorientation is performed by applying the Jacobian affine transform in each voxel in the warp, then re-normalising the vector representing the fixel direction
• fixel_out: the output fixel directory. If the the input and output directories are the same, the existing directions file will be replaced (providing the -force option is supplied). If a new directory is supplied then the fixel directions and all other fixel data will be copied to the new directory.

## Description¶

Reorientation is performed by transforming the vector representing the fixel direction with the Jacobian (local affine transform) computed at each voxel in the warp, then re-normalising the vector.

## Options¶

### Standard options¶

• -info display information messages.
• -quiet do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.
• -debug display debugging messages.
• -force force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).