Camino | Main / Camino file formats (under construction)

This page is a quick reference for the binary file formats produced by various Camino programs. Not all users will need to know the details of the native Camino data files, but it can be useful for troubleshooting and interoperability with other tools. If you are looking for information on scheme files, please see the User Guide. For help importing scanner data into Camino, please see the data import tutorial.

DT

The basic DT type for standard DTI.

Produced by: dtfit, modelfit, restore, wdtfit

Values per voxel: 8

Format: [exitcode, lnA0, dxx, dxy, dxz, dyy, dyz, dzz]

Command line params: -inputmodel dt

Can be converted to NIfTI with dt2nii, and from nifti with niftidt2camino.

Field definition:

exitcode	Encodes information about the reconstruction procedure. -1 means the voxel was skipped as background, 0 indicates success. Positive values mean something went wrong in the reconstruction or some data was modified or excluded. See modelfit for details.
lnA0	Log of the geometric mean of all measurements at b=0 in this voxel.
dxx	D(1,1) = dxx, component of the diffusion tensor.
dxy	D(1,2) = D(2,1) = dxy, component of the diffusion tensor.
dxz	D(1,3) = D(3,1) = dxz, component of the diffusion tensor.
dyy	D(2,2) = dyy, component of the diffusion tensor.
dyz	D(2,3) = D(3,2) = dyz, component of the diffusion tensor.
dzz	D(3,3) = dzz, component of the diffusion tensor.

Multitensor

Gaussian mixture model with maximum of N components per voxel. The maximum number of components, N, is specified by the -maxcomponents option on the command line - it is not encoded in the file. If "-inputmodel multitensor" is passed to a program, N is assumed to be 2 unless otherwise stated.

Produced by: modelfit

Values per voxel: 3 + 7 * N

Format: [exitcode, lnA0, numDTs, N * (mix_i, dxx_i, dxy_i, dxz_i, dyy_i, dyz_i, dzz_i)]

Command line params: -inputmodel multitensor [-maxcomponents 2]

Field definition:

exitcode	Encodes information about the reconstruction procedure. -1 means the voxel was skipped as background, 0 indicates success. Positive values mean something went wrong in the reconstruction or some data was modified or excluded. See modelfit for details.
lnA0	Log of the geometric mean of all measurements at b=0 in this voxel.
numDTs	Number of Gaussian components in this voxel, from 0 to N.
mix_i	Mixing fraction for tensor i, between 0 and 1. Sum of mix_i over all components is 1.
d**_i	Components of the diffusion tensor i, see DT model.

PDs

Peak directions of a spherical function with a maximum of N peaks per voxel. N is specified with the -numpds option, default N=3.

Produced by: sfpeaks

Values per voxel: 6 + N * 8

Format: [exitcode, ln(A(0)), numPeaks, consistent, meanF, stdF, N * (x_i, y_i, z_i, f_i, H00_i, H01_i, H10_i, H11_i)]

Command line params: -inputmodel pds

Field definition:

exitcode	Inherited from the input stream.
lnA0	Inherited from the input stream.
numPeaks	Number of peaks detected in this voxel, between 0 and N.
consistent	1 if number of peaks and peak directions are consistent when the peak search is repeated from a different starting point, zero otherwise.
meanF	Mean value of the spherical function.
stdF	Standard deviation of the spherical function.
[x,y,z]_i	Orientation of the peak i.
f_i	Value of the spherical function at the peak orientation.
H**_i	Hessian of f at the peak.

DTEig

Diffusion tensor eigen system data. Contains no exit code, nor any information on mixing fractions. If the data was produced from multitensor data with a maximum of N components, then there are N eigensystems output per voxel - though some will be zero in voxels where the number of tensors fit to the data is less than N.

Produced by: dteig

Values per voxel: N * 12

Format: [N * (l_1i, e_11i, e_12i, e_13i, l_2i, e_21i, e_22i, e_33i, l_3i, e_31i, e_32i, e_33i)]

Command line params: -inputmodel dteig

Field definition:

l_1i	Largest eigenvalue for component i.
e_11i	x-component of eigenvector corresponding to l_1.
e_12i	y-component of eigenvector corresponding to l_1.
e_13i	z-component of eigenvector corresponding to l_1.
l_2i	Middle eigenvalue for component i.
e_11i	x-component of eigenvector corresponding to l_2.
e_12i	y-component of eigenvector corresponding to l_2.
e_13i	z-component of eigenvector corresponding to l_2.
l_3i	Smallest eigenvalue for component i.
e_11i	x-component of eigenvector corresponding to l_3.
e_12i	y-component of eigenvector corresponding to l_3.
e_13i	z-component of eigenvector corresponding to l_3.

Streamline fiber tract

Produced by: track, procstreamlines

Not voxel based - contains N points

Format: [N, seedIndex, N * (x, y, z) ]

Command line params: -inputmodel raw, -outputtracts raw

Can be converted to VTK with vtkstreamlines

Field definition:

N	Number of points in streamline
seedIndex	Index to the point where tracking was seeded.
x	x-coordinate of point in physical space assuming origin at (0,0,0) and RH coordinate system
y	y-coordinate of point in physical space assuming origin at (0,0,0) and RH coordinate system
z	z-coordinate of point in physical space assuming origin at (0,0,0) and RH coordinate system

The raw streamline format is always 32 bit float, regardless of the -outputdatatype option. The points are described in physical space assuming an origin in the corner of voxel (0,0,0) (this is a computer graphics convention, most imaging conventions would place the origin at the center of a voxel), and further assuming that x increases left->right, y increases posterior->anterior, and z increases inferior->superior. That is, one recovers voxel coordinates by taking i = floor(x / xVoxelSize), and so on for j and k.

This convention is likely to change in future releases of Camino to be more consistent with other imaging software and NIfTI definitions of physical space.

Streamline fiber voxel list

Produced by: track, procstreamlines

Not voxel based - contains N points

Format: [N, seedIndex, N * (i, j, k) ]

Command line params: -inputmodel voxels, -outputtracts voxels

Can be converted to VTK with vtkstreamlines

Field definition:

N	Number of points in streamline
seedIndex	Index to the point where tracking was seeded.
i	Integer index of point in voxel space
j	Integer index of point in voxel space
k	Integer index of point in voxel space

The voxels format is 16-bit signed integer, and lists the integer indices of all N voxels that the streeamline connects. The voxels are defined with spacing derived from the seed image. This loses some spatial resolution of the streamline but can offer a considerable saving in disk space when compressed.

Streamline OOGL object

Produced by: track, procstreamlines

Not voxel based

Format: OOGL VECT

Command line params: -outputtracts oogl, -outputtracts ooglbinary

The OOGL format option, oogl, outputs a LIST of OOGL VECT objects in ASCII format. The colour at each point on the streamline is an RGB vector that describes the local orientation as a combination of red (x), green (y) and blue (z). The ooglbinary option outputs the same objects in the OOGL binary format. These vectors can be read into Geomview.

This option is left for legacy compatibility, but we are unlikely to add further Geomview support. Future development will make use of VTK.

Streamline VTK object

Produced by: vtkstreamlines

Not voxel based

Format: VTK PolyData

The vtkstreamlines program can convert tracts to VTK streamlines and optionally attach scalar values to each point. The tracts are stored in binary format as a PolyData object.