= Filtering Streamlines =

This tool filter streamlines from a *.trk file based on: 
 * a mask; 
 * length; 
 * 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).

-s subsampling number. It will randomly pick a subset of the streamlines in the file. 

 {{attachment:filtering_before.png||height="360px"}}{{attachment:filtering_after.png||height="360px"}}