Command: segmentations

The segmentations command performs functions associated with the Segmentations tool for plane-by-plane interactive segmentation of medical images and other volume data. Users should be aware that there is another, different command named segmentation, which acts on segmentations read from index maps.

See also: Download DICOM, Volume Viewer, Map Eraser, volume mask, ui view, DICOM segmentation tutorial, ChimeraX DICOM Reference, Medical Image toolbar icons:

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Creating and Editing Segmentations

Usage: segmentations  create  map-model   options
Usage: segmentations ( add | remove )  seg-model  [ axis  axial | coronal | sagittal ]  center  i,j  slice  k  radius  r [ minIntensity  min ] [ maxIntensity  max ]
Usage: segmentations ( add | remove )  seg-model   center  i,j,k  radius  r [ minIntensity  min ] [ maxIntensity  max ]
Usage: segmentations mouseModes  on | off 
Usage: segmentations handModes  on | off 

The segmentations create command starts a new segmentation model for the specified map-model (volume data model).

The segmentations add and segmentations remove add or subtract a circular (if 2D) or spherical (if 3D) area from the specified seg-model.

• The operation is in 2D if a slice index k along the normal of the axis (default axial) is supplied, and the center is given as two integers i,j, the horizontal and vertical grid indices within the slice plane.
• The operation is in 3D if the center is given as three integers, i,j,k being the grid indices along X, Y, and Z.

All grid indices start at zero. The radius  r is the radius of the circular or spherical area being added to or subtracted from the segmentation.

The minIntensity  min and maxIntensity  max settings specify the range of data values that can be added to the segmentation model. They apply only to segmentations add and are ignored by segmentations remove. Only those pixels with data values within the specified range will be added even if a larger area is given in the command. The settings are not persistent, in that they apply only to the command(s) in which they appear; when they are omitted from the command, there is no limit on the range of data values that can be added.

The remaining options set/unset button functions associated with Segmentations:

• mouseModes  on | off – assign mouse modes as specified in the Mouse (3D) settings of the Segmentations tool (on), or return to previous assignments (off); the Medical Image toolbar icon toggles between these states.
• handModes  on | off – assign VR hand-controller modes as specified in the VR Controller settings of the Segmentations tool (on), or return to previous assignments (off); the Medical Image toolbar icon toggles between these states.