Brain Imaging & Analysis Center

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

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.

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.

REFIMAGE: If specified, find peak intensity values and voxel locations in REFIMAGE.
If FLAG & 1, REFIMAGE is another ROI mask data set,
If FLAG & 2, REFIMAGE is another dataset with Cluster list; otherwise REFIMAGE is used to find peak intensity values and voxel location.

By default, ROI list is attached to input mask images.

FLAG (values 1-7 specify MODE, values above 7 are flags that can be added to MODE):

* 1 - create a new cluster list; 1 cluster for each group of contiguous voxels
* 2 - compare 2 cluster lists
* 8 - assign cluster ROIs new VALUEs based on REFIMAGE ROIs. For each cluster ROI with peak/center inside a REF ROI, the new cluster ROI value is:
REF_ROI_value * 10 + Clus_within_REF_num For multiple cluster ROIs within the same REF ROI, the Clus_within_REF_num is assigned a value 0-9. If(FLAG&48)==0 these are in first-come order;
* 16 - sort Cluster values LPI → RAS
* 32 - sort Cluster values by cluster size (biggest → smallest)

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

-roi MERGE refimage flag name minvalley minsize mindist

The ROI MERGE command assumes input data set is roi mask image with an ROI cluste list (usually made with ROI CLUSTER command). The ROI MERGE command allows you to modify the input data set and/or its Cluster list.

Merge can be used in different ways (controlled by FLAG).

FLAG (values 1-7 specify MODE, values above 7 are flags that can be added to MODE):

FLAG 1 - Merge adjacent clusters if:
  1) distance bet peaks < MINDIST
  2) stat value in valley between peaks is within MINVALLEY percent of lower peak
  3) smaller cluster contains fewer than MINSIZE voxels
FLAG 2 - Compare input cluster list to REFIMAGE cluster list.\\
FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE.\\
FLAG 4 - Delete clusters with size smaller than MINVALLEY voxels\\
FLAG 5 - Modify cluster index based on REFIMAGE mask\\
           New index is:  REFMASKVALUE * MINVALLEY + I
         where I starts at 1 and increments to ensure each cluster has unique index.
           

REFIMAGE is the reference data set; the type of data depends on FLAG:

FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map)
		 		If REFIMAGE is omitted the VALLEY argument is ignored
FLAG 2 - REFIMAGE is another mask image with attached cluster list.
FLAG 3 - REFIMAGE contains ROI images, typically an Atlas ROI map.
		 

Other FLAG values:

  8 - do not modify input mask image values when editting ROI list;
      by default when ROI clusters are merged or cluster VALUEs are changed,
      the corresponding image voxel values are also changed to match the new cluster VALUEs.
 16 - sort cluster list values by peak location (LPI -> RAS)
 32 - sort cluster list by cluster size (largest to smallest)
				

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

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