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Manpage of niftidt2camino
niftidt2camino
Section: User Commands (1)
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NAME
niftidt2camino - Converts NIFTI-1 tensors to Camino.
SYNOPSIS
niftidt2camino -inputfile [image.nii] [-s0 <file> | -lns0 <file>] [options]
DESCRIPTION
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
NIFTI intensity scaling parameters are applied.
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.
niftidt2camino -inputfile image.nii -bgmask mask.hdr -lns0 lns0.hdr > dt.Bdouble
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.
- -scaleslope <s>
-
A value v in the diffusion tensor is scaled to v * s + i.
This is applied after any scaling specified by the input image.
Default is 1.0.
- -scaleinter <i>
-
A value v in the diffusion tensor is scaled to v * s + i.
This is applied after any scaling specified by the input image.
Default is 0.0.
- -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.
AUTHORS
Philip Cook <camino@cs.ucl.ac.uk>
This program uses the public-domain niftijlib code by Kate Fissell, University of Pittsburgh.
SEE ALSO
scanner2voxel(1), analyzedti(1), metadt2camino(1)
BUGS
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- EXAMPLES
-
- OPTIONS
-
- AUTHORS
-
- SEE ALSO
-
- BUGS
-
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