Filtering Streamlines

This tool filter streamlines from a *.trk that are: (1) outside a mask, (2) shorter than a length threshold, (3) u-shape fibers based on a segmentation file.

Usage

streamlineFilter -i streamlines -o streamlines -l maxLength -r refImage -m mask/segmentation -nu (filter ushape fibers) -s subsample

where -i input streamline.trk file -o output streamline.trk file -l threshold length. Streamlines shorter than a threshold will be removed. -r reference image -m mask image. All streamlines outside the mask will be removed. This input doesn't need to be binary, streamlines passing through voxels with intensity larger than zero will be kept. -nu no ushape fibers. This flag will remove every streamline that starts and ends with the same segmentation label. (-m flag should input a segmentation file for this). -s subsampling number. It will randomly pick a subset of the streamlines in the file.