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--- jvs:fscan:manual:chapter2:align [2013/01/04 17:23]
voyvodic
+++ jvs:fscan:manual:chapter2:align [2023/02/23 18:43] (current)
@@ Line 10: / Line 10: @@
 FLAG (octal values in parenthesis -- combine options by adding values):
-  * 1 (1) - open and display dynamic MutualInformation window
+  * 1 (1) - Fine adjustment
-  * 2 (2) - Coarse adjustment
+  * 2 (2) - Coarse adjustment (if combined with Fine, Coarse runs first)
-  * 4 (4) - NoMove
+  * 4 (4) - open and display dynamic MutualInformation window
-  * 8 (010) - Offset
+  * 8 (010) - Adjust Offset (translation along axis)
-  * 16 (020) - Rotate
+  * 16 (020) - Adjust Rotation (around axis)
-  * 32 (040) - Scale
+  * 32 (040) - Adjust Scaling (along axis)
-  * 64 (0100) - X axis
+  * 64 (0100) - Do X axis adjustments
-  * 128 (0200) - Y axis
+  * 128 (0200) - Do Y axis adjustments
-  * 256 (0400) - Z axis
+  * 256 (0400) - Do Z axis adjustments
-  * 1024 (02000) - Overlay
+  * 512 (01000) - Mask flag -- ignore voxels in current dataset that have low-bit zero
-Default FLAG is 0733: Adjust X,Y,Z axes for Coarse Offset and Rotation (not Scaling), displaying progress window.
+  * 1024 (02000) - Use current image overlay as alignment data set (default if DATASET omitted)
+  * 2048 (04000) - Debug flag -- display mutual information values and single step through alignment
+Default FLAG is 0737: Adjust X,Y,Z axes for Coarse and Fine Offset and Rotation (not Scaling), displaying progress window.
 For each parameter being adjusted, ALIGN tests NSTEPS values (default=5), with NSTEPS/2 values on either side of the starting value. It performs NCYCLES of adjustment (default=3) of all parameters, decreasing the step size on each cycle.

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