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--- jvs:fscan:manual:chapter2:clusters [2017/09/12 22:47]
voyvodic
+++ jvs:fscan:manual:chapter2:clusters [2023/02/23 18:43] (current)
@@ 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 41: / Line 41: @@
 ==== Merging Cluster ROIs ====
--roi MERGE refimage flag name minvalley minsize mindist
+-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
+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.
-(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).
+Merge can be used in different ways depending on the MODE.\\
+  MODE is specifed by name as:
-FLAG (values 1-7 specify MODE, values above 7 are flags that can be added to MODE):
-  FLAG 1 - Merge adjacent clusters if:
+  (none) - don't modify clusters themselves, just do FLAG>=8 options
-) distance bet peaks < MINDIST
+  peaks  - Merge adjacent clusters if:
-) stat value in valley between peaks is within MINVALLEY percent of lower peak
+) distance (in mm) bet peaks < ARG2 (default 40mm)
-) smaller cluster contains fewer than MINSIZE voxels
+) REFIMAGE value in valley between peaks is within ARG1 percent
-  FLAG 2 - Compare input cluster list to REFIMAGE cluster list.
+         (default 60%) of lower peak (iff REFIMAGE specified)
+  lists 2 - Compare input cluster list to REFIMAGE cluster list.
-  FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE.
+    ARG1 is flag:
+- default
-REFIMAGE is the reference data set; the type of data depends on FLAG:
+- compare based on cluster center locs, otherwise compare peak locs
-  FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map)
+- assume cluster lists already compared (idims[7]s)
-			 		If REFIMAGE is omitted the VALLEY argument is ignored
+- don't change cluster values for matched pairs, otherwise change
-  FLAG 2 - REFIMAGE is another mask image with attached cluster list.
+          cluster values so matched clusters have same values; unmatched clusters have unique values.
-  FLAG 3 - REFIMAGE contains ROI images, typically an Atlas ROI map.
+- remove unmatched clusters from list
+	  Matches closest clusters if distance < ARG2 (mindist)
-Other FLAG values:
+          Sets clusters ival[7] to index of the matched cluster.
-- do not modify input mask image values when editting ROI list;
+          Sets vals[8] to distance between cluster peaks (or ctrs)
-        by default when ROI clusters are merged or cluster VALUEs are changed,
+  map   3 - Compare input cluster list to mask ROIs in REFIMAGE.
-        the corresponding image voxel values are also changed to match the new cluster VALUEs.
+    If ARG1 > 0, new cluster voxel value is:
- - sort cluster list values by peak location (LPI -> RAS)
+      REFVALUE * ARG1 + I
- - sort cluster list by cluster size (largest to smallest)
+        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).
+  REFIMAGE is the reference data set; the type of data depends on the MODE:
+    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.\\
+  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)\\

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