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--- jvs:fscan:manual:chapter2:clusters [2015/06/06 19:29] – created voyvodic
+++ jvs:fscan:manual:chapter2:clusters [2020/07/15 15:31] – 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
-  * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel
 ====Creating cluster ROIs====
@@ Line 17: / Line 16: @@
  -roi CLUSTER refimage flag name
-  	Assumes roi mask image as input.
-	Create an ROI list (name=NAME) of clusters where each
+This assumes roi mask image as input.
-	  cluster is defined by its mask value. For each cluster,
+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.
+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
+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.
-The MERGE command assumes that the current image is an ROI mask.
+By default, ROI list is attached to input mask images.
-MERGE edits the ROI list. Merge adjacent clusters if:
+FLAG (values 1-7 specify MODE, values above 7 are flags that can be added to MODE):
-) distance bet peaks < MINDIST
-) stat value in valley between peaks is within MINVALLEY percent of lower peak
+ * 1 - create a new cluster list; 1 cluster for each group of contiguous voxels\\
-) smaller cluster contains fewer than MINSIZE 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 mode refimage flag name arg1 arg2 opflag
+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 depending on the MODE.\\
+  MODE is specifed by name as:
+  (none) - don't modify clusters themselves, just do FLAG>=8 options
+  peaks  - Merge adjacent clusters if:
+) distance (in mm) bet peaks < ARG2 (default 40mm)
+) REFIMAGE value in valley between peaks is within ARG1 percent
+         (default 60%) of lower peak (iff REFIMAGE specified)
+  lists 2 - Compare input cluster list to REFIMAGE cluster list.
+    ARG1 is flag:
+- default
+- compare based on cluster center locs, otherwise compare peak locs
+- assume cluster lists already compared (idims[7]s)
+- don't change cluster values for matched pairs, otherwise change
+          cluster values so matched clusters have same values; unmatched clusters have unique values.
+- remove unmatched clusters from list
+	  Matches closest clusters if distance < ARG2 (mindist)
+          Sets clusters ival[7] to index of the matched cluster.
+          Sets vals[8] to distance between cluster peaks (or ctrs)
+  map   3 - Compare input cluster list to mask ROIs in REFIMAGE.
+    If ARG1 > 0, new cluster voxel value is:
+      REFVALUE * ARG1 + I
+        where I starts at 1 and increments to ensure each cluster has unique index.
+    If ARG2==0, compare based on cluster center locations,
+      otherwise compare peak locations.
+  small 4 - Delete clusters smaller than ARG1 size
+  big   5 - Keep only ARG1 biggest clusters (delete the rest)
+  pairs 6 - filter pairs based on size or distance
+    If ARG1==0, filter based on distance (in mm) between pair peaks
+    If ARG1==1, filter based on distance (in mm) between pair COMs
+    For ARG1 0/1, vals[8] for kept clusters are reset to this distance
+    If ARG1==2, filter based on size (in voxels) of smaller in pair
+    If ARG1==3, filter based on size (in voxels) of larger in pair
+    If ARG1==4, filter based on size (in voxels) summed for pair
+    ARG2 is minimum size/distance to keep.  Pairs that are less than the
+      minumum value are unpaired (cluster remain in lists)
+    (To remove unpaired clusters use "merge lists 0 10" in each list).
-  FLAG: 2 - do not modify input mask image values when editting ROI list
+  REFIMAGE is the reference data set; the type of data depends on the MODE:
-   (i.e. if merging ROI clusters, change merged mask values)
+    peaks - REFIMAGE is a voxel intensity map (e.g. tval map)
+    lists - REFIMAGE is another mask image with attached cluster list.
+    map  - REFIMAGE contains ROI images, typically an Atlas ROI map.
+    pairs - REFIMAGE is another mask image with attached cluster list.
+    REFIMAGE is omitted if mode is SMALL, BIG, or none.
+  As noted above, the meaning of the ARG1, ARG2 options depends on the MODE.
+  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 by cluster size (largest to smallest)
+- sort cluster list by cluster value (smallest to largest)
+- sort cluster list by peak magnitude
+- sort cluster list by peak location (LPI -> RAS)
   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)
+  MINSIZE: (default= 5 voxels)\\
-  MINDIST: (default= 40 mm)
+  MINDIST: (default= 40 mm)\\
 **See Also:**\\
+[[jvs:fscan:manual:chapter2:roi|ROIs]],
+[[jvs:fscan:manual:chapter2:addroi|Create ROIs]],
+[[jvs:fscan:manual:chapter2:addroi|Create ROIs]],
+[[jvs:fscan:manual:chapter2:editroi|Edit ROIs]],
+[[jvs:fscan:manual:chapter2:roistats|ROI Stats]]
 [[jvs:fscan|fScan Home]],
 [[jvs:fscan:manual|fScan Manual]],
 [[jvs:fscan:manual:chapter2|CmdLineOptions]],
 [[jvs:fscan:manual:help|Manual Help]]