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| streamlineFilter -i streamlines -o streamlines -l maxLength -r refImage -m mask/segmentation -nu (filter ushape fibers) -s subsample | streamlineFilter -i input.trk -o output.trk <ouptions> |
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-i input streamline.trk file -o output streamline.trk file |
-i input streamline.trk file (required) -o output streamline.trk file (required) |
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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 <ouptions>
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.