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--- jvs:fscan:manual:chapter2 [2013/04/25 14:35]
voyvodic
+++ jvs:fscan:manual:chapter2 [2021/02/23 19:39]
voyvodic
@@ Line 15: / Line 15: @@
 |[[jvs:fscan:manual:chapter2:quit|quit]]|[[jvs:fscan:manual:chapter2:raw|raw]]|[[jvs:fscan:manual:chapter2:reference|reference]]|[[jvs:fscan:manual:chapter2:regress|regress]]|[[jvs:fscan:manual:chapter2:rename|rename]]|[[jvs:fscan:manual:chapter2:reorder|reorder]]|
 |[[jvs:fscan:manual:chapter2:resample|resample]]|[[jvs:fscan:manual:chapter2:reslice|reslice]]|[[jvs:fscan:manual:chapter2:roi|roi]]|[[jvs:fscan:manual:chapter2:run|run]]|[[jvs:fscan:manual:chapter2:series|series]]|[[jvs:fscan:manual:chapter2:set|set]]|
-|[[jvs:fscan:manual:chapter2:show|show]]|[[jvs:fscan:manual:chapter2:simulate|simulate]]|[[jvs:fscan:manual:chapter2:stability|stability]]|[[jvs:fscan:manual:chapter2:stats|stats]]|[[jvs:fscan:manual:chapter2:stdev|stdev]]|[[jvs:fscan:manual:chapter2:subset|subset]]|
+|[[jvs:fscan:manual:chapter2:show|show]]|[[jvs:fscan:manual:chapter2:simulate|simulate]]|[[jvs:fscan:manual:chapter2:stability|stability]]|[[jvs:fscan:manual:chapter2:stats|stats]]|[[jvs:fscan:manual:chapter2:stdev|stdev]]|[[jvs:fscan:manual:chapter2:resize|resize]]|
 |[[jvs:fscan:manual:chapter2:surface|surface]]|[[jvs:fscan:manual:chapter2:table|table]]|[[jvs:fscan:manual:chapter2:tpictsignal|tpictsignal]]|[[jvs:fscan:manual:chapter2:transform|transform]]|[[jvs:fscan:manual:chapter2:ttest|ttest]]|[[jvs:fscan:manual:chapter2:verbose|verbose]]|
 |[[jvs:fscan:manual:chapter2:wait|wait]]|[[jvs:fscan:manual:chapter2:warp|warp]]|[[jvs:fscan:manual:chapter2:watch|watch]]|[[jvs:fscan:manual:chapter2:writeover|writeover]]| | |
@@ Line 30: / Line 30: @@
 |[[jvs:fscan:manual:chapter2:accumulate|accumulate]]|-A|Accumulate values for calculating means, StDevs, and trial counts|
 |[[jvs:fscan:manual:chapter2:adapt|adapt]]| | |
+|[[jvs:fscan:manual:chapter2:addtime|addtime]]| |Convert 3D images to 4D images|
 |[[jvs:fscan:manual:chapter2:align|align]]| |Auto-align images by optimizing mutual information |
 |[[jvs:fscan:manual:chapter2:ample|ample]]| |Generate AMPLE normalized activation maps and stability plots|
@@ Line 37: / Line 38: @@
 |[[jvs:fscan:manual:chapter2:browse|browse]]| |Select items from a list|
 |[[jvs:fscan:manual:chapter2:chdir|chdir]]| |                            |
+|[[jvs:fscan:manual:chapter2:config|config]]| |Set parameter values at startup|
 |[[jvs:fscan:manual:chapter2:connect|connect]]| |Open an external port connection|
 |[[jvs:fscan:manual:chapter2:convolve|convolve]]| |Convolve images using kernal matrix|
@@ Line 85: / Line 87: @@
 |[[jvs:fscan:manual:chapter2:query|query]]|-q| |
 |[[jvs:fscan:manual:chapter2:quit|quit]]| |  |
+|[[jvs:fscan:manual:chapter2:ramp|ramp]]| |Generate an intensity ramped image along a cardinal axis|
 |[[jvs:fscan:manual:chapter2:raw|raw]]| |Save a copy of the input raw data prior to any processing steps|
 |[[jvs:fscan:manual:chapter2:reference|reference]]|-r|Specify timing information|
@@ Line 92: / Line 95: @@
 |[[jvs:fscan:manual:chapter2:resample|resample]]| | |
 |[[jvs:fscan:manual:chapter2:reslice|reslice]]|-z|Resample a 3-D volume data set|
-|[[jvs:fscan:manual:chapter2:subset|resize]]|-s| |
+|[[jvs:fscan:manual:chapter2:resize|resize]]|-s| |
 |[[jvs:fscan:manual:chapter2:rmap|rmap]]| |Map temporal fluctuations by condition|
 |[[jvs:fscan:manual:chapter2:roi|roi]]|-b|print STDOUT ROI stats|
@@ Line 101: / Line 104: @@
 |[[jvs:fscan:manual:chapter2:simulate|simulate]]|-y| |
 |[[jvs:fscan:manual:chapter2:stability|stability]]|-d|Generate plots of changes in image position and intensity|
+|[[jvs:fscan:manual:chapter2:start|start]]| |Specify fScan one-time start-up options|
 |[[jvs:fscan:manual:chapter2:stats|stats]]| |Calculate simple mean, stdev, and count statistics|
 |[[jvs:fscan:manual:chapter2:stdev|stdev]]|-V|Generate variance images|

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