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--- jvs:fscan:manual:chapter2:roi [2016/07/26 20:03]
voyvodic
+++ jvs:fscan:manual:chapter2:roi [2023/02/23 18:43] (current)
@@ Line 19: / Line 19: @@
   * -roi FILE roifile
   * -roi RX refimage  (not yet implemented)
-  * -roi MEAN flag
+  * -roi AVERAGE flag radiusMM thresh
+  * -roi HEAD [NAME] flag
+     Create BLOCK roi by auto-detection of top, sides, & front/back of head.
+     Arbitrarily set bottom by making I-S distance same as R-L.
+      FLAG: 0 - default (bottom boundary set at top - (L/R distance)
+-
+- set intensity threshold at 10% of maxval (default is 15%)
+- set     "         "     "  20%
+             ...
+- set     "         "     "  70%
+  * -roi ALIGN [refimage flag refroi thisroi]
+     Generate affine matrix (align or wsalaign) to align current images
+     to REFIMAGE dataset by scaling and translating THISROI to match REFROI.
+       REFIMAGE - data set to align to (prevwin by default)
+       FLAG - option flag (default = 0)
+       REFROI - name or ROINUM for REFIMAGE roi to use
+                (default is active or first ROI)
+       THISROI - name or ROINUM for current image roi
+                (default is active or first).
+     Example usage is to align head rois (see: -roi HEAD)
 [[jvs:fscan:manual:chapter2:roicorrel|Generate ROI correlations]]\\
   * -roi CORREL flag refROI binsize corrROI name thresh
 [[jvs:fscan:manual:chapter2:clusters|Cluster ROIs]]\\
   * -roi CLUSTER refimage flag name
   * -roi MERGE refimage flag name minvalley minsize mindist
 [[jvs:fscan:manual:chapter2:roistats|Generate ROI statistics]]\\
   * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel
@@ Line 55: / Line 80: @@
 	NAME: name of ROI list. If omitted, list is linked to
           input mask images.
--roi MERGE refimage flag name minvalley minsize mindist
+-roi MERGE refimage flag name minval minsize mindist
-The MERGE command assumes that the current image is an ROI mask.
+Assumes input data set is roi mask image with an ROI 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 edits the ROI list. Merge adjacent clusters if:
+Merge can be used in different ways (controlled by FLAG):
-) distance bet peaks < MINDIST
-) stat value in valley between peaks is within MINVALLEY percent of lower peak
+  FLAG 1 - Merge adjacent clusters if:
-) smaller cluster contains fewer than MINSIZE voxels
+) distance bet peaks < MINDIST
+) stat value in valley between peaks is within MINVAL percent of lower peak
+) smaller cluster contains fewer than MINSIZE voxels
+  FLAG 2 - Compare input cluster list to REFIMAGE cluster list.
-  FLAG: 2 - do not modify input mask image values when editting ROI list
+  FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE.
-   (i.e. if merging ROI clusters, change merged mask values)
-  NAME: name of ROI list. If omitted, list is linked to input mask images.
+  REFIMAGE is the reference data set; the type of data depends on FLAG:
-  MINVALLEY: (default= 60% of lower peak maximum)
+    FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map)
-  MINSIZE: (default= 5 voxels)
+    FLAG 2 - REFIMAGE is another mask image with attached cluster list.
-  MINDIST: (default= 40 mm)
+    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; 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 values by peak location (LPI -> RAS)
+- sort cluster list by cluster size (largest to smallest)
+  NAME: name of ROI list. If omitted, list is linked to input mask images.
 -roi STATS refimage flag showflag mode name value nlevels level0 dlevel\\
 -roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh  (if flag TIMESERIES)
@@ Line 120: / Line 163: @@
   NAME - save stats in file NAME, if specified
   VAL: if > 0, only calculate for this mask value
   If FLAG & 02010, time-series by CYCLE,
     CYCLELENG: task cycle length in secs
@@ Line 129: / Line 172: @@
     LEVEL0: first threshold level (def=0)
     DLEVEL: increment between levels (def=1)
-If input is a Surface:
+  If input is a Surface:
   FLAG
 - surface area of AREA ROI or path length of contour ROI

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