tracktion_notes.txt

This software can create streamlines from FSL V1/FA files.

Advantages:
-Preserves spatial orientation
-Creates streamlines in popular formats (VTK, bfloat, trk, bfloat.gz, trk.gz)
-Allows you to restrict streamlines to those that traverse voxel-defined waypoints
-Very fast

Limitation:
-FSL V1 files do not allow us to solve crossing fibers
-In regions of low FA, FSL defaults to having fibers pointing left-right, causing 'ghost fibers' (solution: do not reduce FA threshold too much).
-Linear interpolation does not work well for FSL V1 maps

To do:
-Compute measures that allow fiber crossing
-Erode/dilate waypoints


**EXAMPLES**

Default option (use M2165_FA and M2165_V1 to create M2165.vtk)
./tracktion  M2165

Draw streamlines for whole brain (9 fibers per voxel)
./tracktion  -5 9 -t 0.2 -4 0.3 -o high-res.trk.gz  M2165

Draw streamline for whole brain (9 fibers per voxel)
./tracktion  -w M2165_ROI CorpusCallosum.trk  M2165


Identify fibers that traverse both left and right splenium waypoints
./tracktion -w M2165_jhu.nii,128 -w M2165_jhu.nii,127 -o Splenium.trk  M2165


**FULL HELP**
Tracktion by Chris Rorden version 19Sept2016
Usage: tracktion [options] basename
 Requires dtifit V1 FA images (basename_V1.nii.gz, basename_FA.nii.gz)
Options
 -a maximum angle bend (degrees, default 45)
 -h show help
 -l minimum length (mm, default 12)
 -o output name (.bfloat, .bfloat.gz or .vtk; default "inputName.vtk")
 -s simplification tolerance (mm, default 0.2)
 -t fa threshold (default 0.15)
 -w waypoint name (up to 8; default: none)
 -1 smooth (0=not, 1=yes, default 1)
 -2 stepsize (voxels, voxels 0.5)
 -3 minimum steps (voxels, default 1)
 -4 redundant fiber removal threshold (mm, default 0)
 -5 seeds per voxel (default 1)
Examples
 tracktion -t 0.2 -o "~/out/fibers.vtk" "~/img_V1.nii.gz"
 tracktion -w BA44.nii -w BA44.nii "~/img_V1.nii"