Differences

This shows you the differences between two versions of the page.

--- jvs:fscan:manual:chapter2:clusters [2015/06/06 19:29]
voyvodic created
+++ 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
-  * -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:
-  FLAG: 2 - do not modify input mask image values when editting ROI list
+  (none) - don't modify clusters themselves, just do FLAG>=8 options
-   (i.e. if merging ROI clusters, change merged mask values)
+  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).
+  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.
-  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]]

Brain Imaging & Analysis Center

User Tools

Site Tools

Differences

Page Tools