mincdefrag

remove small disconnected fragments from a labelled MINC volume

mincdefrag input.mnc output.mnc label stencil [max_connect]

DESCRIPTION

mincdefrag removes small disconnected fragments of a specified label from a labelled MINC volume. The program identifies connected components of voxels with the given label value and removes components that contain fewer voxels than the max_connect threshold by replacing them with the most common neighbouring label.

The label argument specifies the integer label value of the voxels to process. The stencil argument defines the connectivity neighbourhood: 6 for face-connected neighbours, 19 for face- and edge-connected neighbours, or 27 for face-, edge-, and corner-connected neighbours.

The optional max_connect parameter sets the minimum number of connected voxels required for a component to be retained. Components smaller than this threshold are removed.

EXAMPLES

Remove small fragments of label 3 using 6-connectivity:

mincdefrag labels.mnc cleaned.mnc 3 6

Remove fragments smaller than 100 voxels using 26-connectivity:

mincdefrag labels.mnc cleaned.mnc 3 27 100

SEE ALSO

dilate_volume, mask_volume, mincmorph

AUTHOR

David MacDonald - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

COPYRIGHTS

Copyright © 1996 by David MacDonald