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--- jvs:fscan:manual:chapter2:clusters [2017/09/12 23:02]
voyvodic
+++ jvs:fscan:manual:chapter2:clusters [2017/12/08 18:11]
voyvodic
@@ Line 64: / Line 64: @@
   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 or 5 - REFIMAGE contains ROI images, typically an Atlas ROI map.
+  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;
@@ Line 74: / Line 79: @@
 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)\\

Brain Imaging & Analysis Center