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--- jvs:fscan:manual:chapter2:stability [2011/04/29 21:17] – voyvodic
+++ jvs:fscan:manual:chapter2:stability [2017/02/14 21:27] – voyvodic
@@ Line 1: / Line 1: @@
 **fScan Reference Manual, Chapter 2 (CmdLineOptions): stability**
 ===== Stability -- Calculate displacements of center-of-mass=====
-**usage:** -stability flag outname refimg slice maxpct
+**usage:** -stability flag outname refimg slice maxpct levelmm levelpct1 levelpct2
 ===== =====
   * FLAG - can take on the following values:
@@ Line 8: / Line 8: @@
     * 2 - generate dx/dy/di plots for each slice separately
     * 4 - censor images where dx or dy is greater than MAXPCT
-    * 8 - use the most frequent position as reference (otherwise use mean value)
+    * 8 - print volume motion parameters
+    * 16 - print image motion parameters
+    * 32 - motion censor data by volume (default is by image)
     * 64 - report global X/Y motion values (mean, stdev, max)
+    * 128 - use the most frequent position as reference (otherwise use mean value)
+    * 512 - create a point ROI at the image center-of-mass for the central timepoint
     * 3 - generate all plots (default)
   * REFIMG - reference time point for image registration (default=0)
   * SLICE - If specified, only that slice is done, otherwise all.
-  * MAXPCT - Used when motion censoring (FLAG & 4). Images with displacement greater than MAXPCT of a voxel will be omitted from further analysis (default MAXPCT = 25%).
+  * MAXPCT - Used when motion censoring (FLAG & 4). Images with displacement greater than MAXPCT of a voxel will be omitted from further analysis (default MAXPCT = 50% for images, 30% if censoring volumes(flag 32)).
+  * LEVELMM - minimum motion level for reporting percent of images moved (default: 1 mm)
+  * LEVELPCT1 - (default: 5)
+  * LEVELPCT2 - (default: 20)
 **See Also:**\\