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--- jvs:fscan:manual:chapter2:clusters [2017/09/12 23:00]
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
 ====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):
+  (none) - don't modify clusters themselves, just do FLAG>=8 options
-  FLAG 1 - Merge adjacent clusters if:
+  peaks  - Merge adjacent clusters if:
-) distance bet peaks < MINDIST
+) distance (in mm) bet peaks < ARG2 (default 40mm)
-) stat value in valley between peaks is within MINVALLEY percent of lower peak
+) REFIMAGE value in valley between peaks is within ARG1 percent
-) smaller cluster contains fewer than MINSIZE voxels
+         (default 60%) of lower peak (iff REFIMAGE specified)
-  FLAG 2 - Compare input cluster list to REFIMAGE cluster list.\\
+  lists 2 - Compare input cluster list to REFIMAGE cluster list.
-  FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE.\\
+    ARG1 is flag:
-  FLAG 4 - Delete clusters with size smaller than MINVALLEY voxels\\
+- default
-  FLAG 5 - Modify cluster index based on REFIMAGE mask\\
+- compare based on cluster center locs, otherwise compare peak locs
-             New index is:  REFMASKVALUE * MINVALLEY + I
+- assume cluster lists already compared (idims[7]s)
-           where I starts at 1 and increments to ensure each cluster has unique index.
+- don't change cluster values for matched pairs, otherwise change
+          cluster values so matched clusters have same values; unmatched clusters have unique values.
-REFIMAGE is the reference data set; the type of data depends on FLAG:
+- remove unmatched clusters from list
-  FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map)
+	  Matches closest clusters if distance < ARG2 (mindist)
-			 		If REFIMAGE is omitted the VALLEY argument is ignored
+          Sets clusters ival[7] to index of the matched cluster.
-  FLAG 2 - REFIMAGE is another mask image with attached cluster list.
+          Sets vals[8] to distance between cluster peaks (or ctrs)
-  FLAG 3 - REFIMAGE contains ROI images, typically an Atlas ROI map.
+  map   3 - Compare input cluster list to mask ROIs in REFIMAGE.
+    If ARG1 > 0, new cluster voxel value is:
-Other FLAG values:
+      REFVALUE * ARG1 + I
-- do not modify input mask image values when editting ROI list;
+        where I starts at 1 and increments to ensure each cluster has unique index.
-        by default when ROI clusters are merged or cluster VALUEs are changed,
+    If ARG2==0, compare based on cluster center locations,
-        the corresponding image voxel values are also changed to match the new cluster VALUEs.
+      otherwise compare peak locations.
- - sort cluster list values by peak location (LPI -> RAS)
+  small 4 - Delete clusters smaller than ARG1 size
- - sort cluster list by cluster size (largest to smallest)
+  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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