Hello, I am new to DTI tractography, and I am trying to use fsl-fdt probtrackX command to save streamlines after bedpostX.
However, the default output file fdt_path.nii.gz is volume data, I want 3-dim streamline vectors instead for subsequent fiber clustering. I did some readings, probtrackx2 has a --savepaths option that seems to work, but I tried and failed. Could anyone help me out? Do I need to use external tools or write my own scripts to do this?
Thank you in advance!
My team’s nii_preprocess includes compiled copies of our tracktion software for macOS and Linux that can create streamlines in BEDPOSTX dyads files. I would look carefully at the release notes. We use these for visual inspection of streamlines using Surfice for QA purposes only, and use other tools to estimate link strength between cortical nodes.
Assuming you have lazarus installed, you could compile a copy like this:
git clone https://github.com/neurolabusc/surf-ice.git
cd surf-ice
lazbuild -B tracktion.lpr
./tracktion
Tracktion by Chris Rorden version 14Feb2017
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 threshold (FA for dtifit, probability for bedpost) (default 0.15)
-w waypoint name (up to 8; default: none)
-x bedpost exponent (0=sample p1/p2 equally, 2=strongly prefer p1, default 0.5)
-1 smooth (0=no, 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 BA3.nii "~/img_V1.nii"
tracktion dyads1.nii.gz
Many thanks for your reply, Chris! I definitely want to try nii_preprocess out!
MANAGED BY INCF