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--- jvs:fscan:manual:chapter2:expression:censor [2017/06/02 19:15]
voyvodic
+++ jvs:fscan:manual:chapter2:expression:censor [2023/02/23 18:43] (current)
@@ Line 1: / Line 1: @@
 **fScan Reference Manual, Chapter 2 (CmdLineOptions:Expr): censor**
-===== censor -- =====
+===== censor -- replace or remove selected images from time series =====
- **usage:  -expr censor [timeref] [flag]**\\
+ **usage:  -expr censor [timeref] [flag [filloption]]**
-	 -expr censor [ref] [flag [fillindex] [fillimages]]
+CENSOR replaces flagged with new values, or it can completely remove images. Which images to censor is controlled by a reference time series. By default, the reference time series is the data set's "ACTIVE" reference timeline (0/1 value for each image).  Alternatively, a reference time series can be specified explicitly by name as the first argument (TIMEREF).
-CENSOR replaces flagged time points with new values. By default, time points are flagged using the data set's "ACTIVE" reference timeline (0/1 value for each image).  Alternatively, time points can be flagged by explicitly specifying a reference time course (TIMEREF).
+Usually the reference series should have at least as many values as their are images, in which case the images to be censored are those for which the corresponding reference value is less than or equal to zero (any positive reference value means keep that image).
-All voxels in images with a 0 reference value will be replaced according the the FLAG argument, as:\\
+Alternatively, if the FLAG argument includes the 8 option, then the reference series is assumed to be an explicit list of which image numbers to censor. Image numbering always starts with 0 for the first image of the first volume, then the 2nd image of the first volume, etc. For example, if a data set has 20 image slices per volume and TIMEREF has values [ 0, 4, 107 ] then the only images to be censored would be: slice 0 volume 0, slice 4 volume 0, and slice 7 volume 4. Such a TIMEREF must contain only unique values sorted in ascending order; the list can be any length up to the total number of images.
-FLAG:\\
-  * 0 - replace with linear interpolation of surrounding time points (default)
-  * 1 - replace with spline interpolation of surrounding time points
-  * 2 - replace with zeros
-  * 3 - excise the value (result is fewer time points)
-Other FLAG values can be combined with the above byb addition:\\
+What happens to censored images depends on the values of the FLAG and FILLOPTION arguments. FILLOPTION can be a number, indicating which image volume of the data being censored to use as fill images, or it can be the name of a 3D image data set (with the same XYZ dimensions as the data being censored).
-  * 4 - adjust values after 0 reference values to have similar means to earlier values (matches means of 3 values before and after)
-  * 8 - The TIMEREF is a list of time point indices to censor (default is TIMEREF is 0/1 flag for every timepoint)
-  *   adjust values after censored values to have similar means to earlier values (matches means of 3 values before and after)
-				/* val:  0 - (default) replace with linear interpolation; or
+FLAG - censoring operation:\\
-				             same as VAL=8 if VAL2 is non-zero
+ * 0 - replace with linear interpolation (unless FILLOPTION specified) \\
-- replace with spline interpolation
+ * 1 - replace with spline interpolation\\
-- replace with 0's
+ * 2 - replace with zeros (blank image)\\
-- excise
+ * 3 - remove image entirely making shorter image series (blank images added at end)\\
-- match post-mean to pre-mean
+ * 4 - match post-mean to pre-mean\\
-- replace with value at 1st censored timept at or after timept VAL2
+ * 8 - reference is list of image numbers to remove; otherwise is 0/1 flag\\
- - replace with value at 1st uncensored timept at or after VAL2
+ * 16 - replace with value at 1st censored time point at or after timept FILLOPTION\\
- - replace with value at timept VAL2
+ * 17 - replace with value at 1st uncensored time point at or after FILLOPTION\\
- - active is t-index; otherwise is 0/1 flag
+ * 18 - replace with value at time point FILLOPTION\\
+ * 32 - replace with FILLOPTION data set images\\
+Default FLAG is:\\
+ * 0 if FILLOPTION is 0 or not specified, or\\
+ * 16 if FILLOPTION is a number, or\\
+ * 32 if FILLOPTION is data set name
 **See Also:**\\

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