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← Revision 11 as of 2018-09-30 15:28:48 ⇥
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| 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. | This tool filter streamlines from a *.trk file based on: * a mask; * length; * u-shape fibers based on a segmentation file.; |
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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 <options> }}} where |
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| where -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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| -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). | -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). |
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{{attachment:filtering_before.png||height="360px"}}{{attachment:filtering_after.png||height="360px"}} |
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.
