This tool converts NIFTI-1 diffusion tensors to Camino format. The program reads the
NIFTI header but does not apply any spatial transformations to the data.
The output is the tensors in Camino voxel ordering: [exit, ln(S0), dxx, dxy, dxz, dyy,
dyz, dzz].
The exit code is set to 0 unless a background mask is supplied, in which case the code is
0 in brain voxels and -1 in background voxels.
The value of ln(S0) in the output is taken from a file if one is supplied, otherwise it
is set to 0.
NOTE FOR FSL USERS - FSL's dtifit can output NIFTI tensors, but they are not stored in
the usual way (which is using NIFTI_INTENT_SYMMATRIX). FSL's tensors follow the ITK / VTK
"upper-triangular" convention, so you will need to use the -uppertriangular option
to convert these correctly.
EXAMPLES
Convert tensors from the file image.nii, applying a brain / background segmentation
including the unweighted signal in the output.
Alternatively, the output may be piped to any Camino program that takes tensors as input.
OPTIONS
-inputfile <niftifile>
A NIFTI-1 dataset containing diffusion tensors. The tensors are assumed to be in
lower-triangular order as specified by the NIFTI standard for the storage of symmetric
matrices. This file should be either a .nii or a .hdr file.
-s0 <file>
File containing the unweighted signal for each voxel, may be a raw binary file(specify
type with -inputdatatype) or a supported image file.
-lns0 <file>
File containing the log of the unweighted signal for each voxel, may be a raw binary file
(specify type with -inputdatatype) or a supported image file.
-bgmask <mask>
Binary valued brain / background segmentation, may be a raw binary file (specify type
with -maskdatatype) or a supported image file.
-uppertriangular
Specifies input in upper-triangular (VTK style) order. The NIfTI symmatrix intent code
specifies lower triangular, which is the default, this option lets you override that if
needed.