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--- jvs:fscan:manual:chapter2:clusters [2016/07/26 20:03] – voyvodic
+++ jvs:fscan:manual:chapter2:clusters [2017/12/08 18:11] – voyvodic
@@ Line 3: / Line 3: @@
 ====usage:====
   * -roi CLUSTER refimage flag name
-  * -roi MERGE refimage flag name minvalley minsize mindist
+  * -roi MERGE refimage flag name minval minsize mindist
 ====Creating cluster ROIs====
@@ Line 20: / Line 20: @@
 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.
+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: (no values yet)
+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.
+==== Merging Cluster ROIs ====
 -roi MERGE refimage flag name minvalley minsize mindist
-The MERGE command assumes that the current image is an ROI mask.
+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 edits the ROI list. Merge adjacent clusters if:
+Merge can be used in different ways (controlled by FLAG).
-  * distance bet peaks < MINDIST
-  * stat value in valley between peaks is within MINVALLEY percent of lower peak
+FLAG (values 1-7 specify MODE, values above 7 are flags that can be added to MODE):
-  * smaller cluster contains fewer than MINSIZE voxels
+  FLAG 1 - Merge adjacent clusters if:
+) distance bet peaks < MINDIST
-FLAG: 2 - do not modify input mask image values when editting ROI list
+) stat value in valley between peaks is within MINVAL percent of lower peak
-(i.e. if merging ROI clusters, change merged mask values)
+) 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 MINVAL voxels
+  FLAG 5 - Modify cluster index based on REFIMAGE mask
+             New index is:  REFMASKVALUE * MINVAL + 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)
+  FLAG 2 - REFIMAGE is another mask image with attached cluster list.
+  FLAG 3 - REFIMAGE contains ROI images, typically an Atlas ROI map.
+  FLAG 4 - Remove clusters containing less than MINVAL voxels
+  FLAG 5 - Use REFIMAGE to adjust cluster index values. For each cluster,
+           find REFIMAGE mask value (REFVALUE) at cluster center. New cluster index is:
+                   REFVALUE * MINVAL + I
+           where I starts at 1 and increments to ensure each cluster has unique index.
+Other FLAG values:
+- 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.
+- sort cluster list values by peak location (LPI -> RAS)
+- 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)\\
+MINVAL: (default= 60% of lower peak maximum)\\
 MINSIZE: (default= 5 voxels)\\
 MINDIST: (default= 40 mm)\\
@@ Line 46: / Line 85: @@
 **See Also:**\\
+[[jvs:fscan:manual:chapter2:roi|ROIs]],
 [[jvs:fscan:manual:chapter2:addroi|Create ROIs]],
 [[jvs:fscan:manual:chapter2:addroi|Create ROIs]],