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jvs:fscan:manual:chapter2:clusters

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fScan Reference Manual, Chapter 2 (CmdLineOptions): clusters

ROI -- Define and manipulate Cluster Regions of Interest

usage:

  • -roi CLUSTER refimage flag name
  • -roi MERGE refimage flag name minvalley minsize mindist

Creating cluster ROIs

The CLUSTER type ROI assumes that the current data set is an ROI mask image (in which regions are defined by voxels with the same intensity value). The CLUSTER command uses the input mask image to create an ROI list (name=NAME) of CLUSTER type ROIs where each cluster is defined by its mask value. For each CLUSTER, the center-of-mass location and the radius along the 3 principal axes are stored. By default, the new ROI list is attached to the input mask data set.

  • REFIMAGE, find peak intensity value and voxel location.
  • FLAG: (no values yet)
  • NAME: name of ROI list. If omitted, the list is linked to input mask images.

Manipulating cluster ROIs

The ROI command can also be used to manipulate existing ROI's.

-roi CLUSTER refimage flag name

This assumes roi mask image as input. It creates an ROI list (name=NAME) of clusters where each cluster is defined by its mask value. For each cluster, store center-of-mass and radius along principal axes. If REFIMAGE, find peak intensity value and voxel location. By default, ROI list is attached to input mask images.

FLAG: (no values yet)

NAME: name of ROI list. If omitted, list is linked to input mask images.

-roi MERGE refimage flag name minvalley minsize mindist

The MERGE command assumes that the current image is an ROI mask.

MERGE edits the ROI list. Merge adjacent clusters if:

  • distance bet peaks < MINDIST
  • stat value in valley between peaks is within MINVALLEY percent of lower peak
  • smaller cluster contains fewer than MINSIZE voxels

FLAG: 2 - do not modify input mask image values when editting ROI list (i.e. if merging ROI clusters, change merged mask values)

NAME: name of ROI list. If omitted, list is linked to input mask images.
MINVALLEY: (default= 60% of lower peak maximum)
MINSIZE: (default= 5 voxels)
MINDIST: (default= 40 mm)

See Also:
ROIs, Create ROIs, Create ROIs, Edit ROIs, ROI Stats

fScan Home, fScan Manual, CmdLineOptions, Manual Help

jvs/fscan/manual/chapter2/clusters.1469563558.txt.gz · Last modified: 2016/07/26 20:05 by voyvodic