maps tractogram features on an image


./trekker track2img [OPTIONS] <input tractogram> <output image>


  • <input tractogram> TEXT:FILE REQUIRED Input tractogram (.vtk, .tck)

  • <output image> TEXT REQUIRED Output image name (.nii, .nii.gz)


Option Description
--feature TEXT Name of output feature. Options are: "streamlineCount", "segmentLength" or "DEC_SegmentLength".
--weights TEXT:FILE A binary file for streamline weights. Values should have float datatype.
--anisotropicSmoothing [FLOAT,INT] Standard deviation of the Gaussian kernel, and computation density for anisotropic smoothing. Default=0 0.
--SF INT Spherical domain detail. This value should be a positive odd integer up to 31.
--SF_smoothing FLOAT Apply spherical smoothing.
--SH INT Order of spherical harmonics function. Only even orders are supported.
-t, --template TEXT:FILE Input template image (.nii/.nii.gz).
--templateUpsample FLOAT Upsampling factor for template image.
-b, --bbox FLOAT ... Bounding box for the output image.
Options are:
(i) "x_min x_max y_min y_max z_min z_max" (an isotropic voxel dimension of 1 will be assumed.)
(ii) "x_min x_max y_min y_max z_min z_max voxDim" (an isotropic voxel dimension of voxDim will be assumed.)
(iii) "x_min x_max y_min y_max z_min z_max xVoxDim yVoxDim zVoxDim"
--voxDim FLOAT ... Voxel dimension of the output image.
Options are:
(i) a single value that will be used for all dimensions
(ii) one value for each of the three dimensions separated by space.
--mask TEXT:FILE Input mask image (.nii/.nii.gz).
--maskLabel INT Label to use in the mask image.

General options

Option Description
-h, --help Print this help message and exit.
-n, --numberOfThreads INT Number of threads.
-v, --verbose TEXT Verbose level. Options are "quiet", "fatal", "error", "warn", "info", and "debug". Default=info.
-f, --force Force overwriting of existing file.


For uses without spherical mapping, please cite [Calamante2010], which provides detailed information on Track-density imaging (TDI).

For uses with spherical mapping, please cite [Dhollander2014], which explains Track Orientation Density Imaging (TODI) and Track Orientation Distribution (TOD) based tractography.