apply spatial transformations or reslice images.
| -transform transform | specified the 4x4 transform to apply. 
| transform | the transform to apply, in the form of a 4x4 ascii file. |  | 
| -replace | replace the current transform by that specified, rather than applying it to the current transform. | 
| -inverse | invert the specified transform before using it. | 
| -template image | reslice the input image to match the specified template image. 
| image | the template image. |  | 
| -reference image | in case the transform supplied maps from the input image onto a reference image, use this option to specify the reference. Noe that this implicitly sets the -replace option. 
| image | the reference image. |  | 
| -flipx | assume the transform is supplied assuming a coordinate system with the x-axis reversed relative to the MRtrix convention (i.e. x increases from right to left). This is required to handle transform matrices produced by FSL's FLIRT command. This is only used in conjunction with the -reference option. | 
| -info | display information messages. | 
| -quiet | do not display information messages or progress status. | 
| -debug | display debugging messages. | 
| -help | display this information page and exit. | 
| -version | display version information and exit. |