track2img¶
maps tractogram features on an image
Usage
./trekker track2img [OPTIONS] <input tractogram> <output image>
Positionals
<input tractogram> TEXT:FILE REQUIRED Input tractogram (.vtk, .tck)
<output image> TEXT REQUIRED Output image name (.nii, .nii.gz)
Options
| 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. |
References
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.
