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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 input.trk -o output.trk <options>

where

-i input streamline.trk file (required)

-o output streamline.trk file (required)

-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.