Differences

This shows you the differences between two versions of the page.

--- jvs:fscan:manual:chapter3:surfkeys:objects [2011/11/09 19:27]
voyvodic created
+++ jvs:fscan:manual:chapter3:surfkeys:objects [2014/03/25 20:43]
voyvodic
@@ Line 1: / Line 1: @@
-select object (e.g. fiber track) filters */
+**fScan Reference Manual, Chapter 3 (KeyCmds:SurfKeys): objects **
-/* usage: 'NAME',mode,value,param,flag T
+===== Objects -- Manipulate surface object display properties =====
-NAME - modes 0-2: ROI mask image (default is previous window)
+**usage: 'NAME',mode,value,param,flag T**
-NAME - mode 5: object param subset name
-NAME - mode 7: new data set name
+The surface objects commands ('T') allow you to select and manipulate 3D objects (e.g. fiber tracks).
-MODE - operation
-- turn off PARAM bit(s) for fibers in ROI VALUE voxels
+NAME: the meaning of this argument varies depending on the MODE\\
-PARAM default=1
+  * modes 0-2: ROI mask image (default is previous window)
-FLAG: 0 - set all fibers
+  * mode 5: object param subset name
-- VAL is ROI num if ROIs, else intensity (default)
+  * mode 7: new data set name
-- VAL is intensity value
-- turn on PARAM bit(s) for fibers in ROI VALUE voxs
+The MODE argument controls what type of object command to perform.\\
-PARAM and FLAG same as mode 0.
+MODE:\\
-- turn off PARAM for active fibers not passing through ROI
+  * 0 - turn off PARAM bit(s) for objects in ROI
-PARAM and FLAG same as mode 0.
+    * NAME - ROI mask image (default is previous window)
-- in/activate fibers where (param&VALUE) == PARAM
+    * VALUE - index of ROI region (see FLAG)
-If PARAM==0, then where (param&VALUE).
+    * PARAM - bit value in object parameter (default=1)
-If FLAG==0 inactivate, else activate
+    * FLAG:
-- in/activate fibers with at least VALUE points
+      * 0 - set all objects
-(or less than VALUE if PARAM&1)
+      * 1 - VALUE is ROI num if ROIs, else intensity (default)
-If FLAG==0 inactivate, else activate
+      * 2 - VALUE is intensity value
-- set/clear param for tracks where ??
+      * 4 - include only objects with endpoint in ROI (default includes objects intersecting ROI)
-- save active objects as new data set
+  * 1 - turn on PARAM bit(s) for objects in ROI
-- set OBJFLAG to ROIVALUE
+    * NAME, VALUE, PARAM, and FLAG same as mode 0.
-- set OBJMASK to ROIVALUE
+  * 2 - turn off PARAM for active objects not passing through ROI
-Note: track param bit 1 means track is active
+    * NAME, VALUE, PARAM, and FLAG same as mode 0.
-ROIVALUE - index value in ROI mask
+  * 3 - in/activate objects based on parameter value (ObjectParam) stored with each
-- all voxels
+    * PARAM - mask flag
+      * 0 - in/activate where (ObjectParam & VALUE) is non-zero.
+      * >0 - in/activate where (ObjectParam & VALUE) == PARAM.
+    * FLAG - If 0 inactivate, else activate
+  * 4 - in/activate objects based on number of data points
+    * PARAM - Control flag
+      * 0 - objects with at least VALUE points
+      * 1 - objects with less than VALUE points
+      * FLAG - If 0 inactivate, else activate
+  * 5 - set/clear param for objects where ??
+    * NAME - object param subset name
+  * 7 - save active objects as new data set
+    * NAME - new data set name
+  * 8 - set OBJFLAG to VALUE
+    * If VALUE is omitted this displays current OBJFLAG value
+  * 9 - set OBJMASK to VALUE
+    * If VALUE is omitted this displays current OBJMASK value
+  * 10 - set NUMFASTOBJECTS to VALUE
+    * If VALUE is omitted this displays current NUMFASTOBJECTS value
+    * If NUMFASTOBJECTS is positive, that many fibers will be displayed in [[jvs:fscan:manual:chapter3:surfkeys:flags|Fast]] mode
+  * 11 - generate object parameter values by sampling associated images at each object vertex
+    * NAME: reference image (default is prev window)
+    * VALUE:
+      * 1 - FA values (1/vtx)
+      * 2 - ADC values (1/vtx)
+      * 3 - track length values (mm), 1/track
+      * 4 - length (npts) histogram of active objects
+  * 12 - generate new data set with objects as avg of all active objects connected to each ROI (1/ROI). This assumes active objects already seed selected.
+    * NAME: ROI image (default is all active objects)
+    * VALUE: Averaged values (bitmask)
+      * 1 - # of source objects (1/obj)
+      * 2 - length of tracks mm (1/obj) + StDev
+      * 4 - total average param values (1/obj) + SD
+      * 8 - average param 1/mm (1/vtx)
+      * 16 - stdev for each 1/vtx param avgs
+      * 32 - # objects along path (1/vtx)
+    * PARAM: Selection options:
+      * 1 - selected tracks connected to each ROI
+      * 2 - selected tracks connecting all pairs of ROI's (default)
+      * 4 - include tracks passing through target ROI (default is endpt in ROI)
+  * 20 - set NOBJECTS to VALUE
+  * 21 - set NCOORDS to VALUE
+Notes:\\
+Track param bit 1 means track is active\\
+ROIVALUE - index value in ROI mask\\
+  * 0 - all voxels
+  * >0 - voxels with value ROIVALUE
+Examples:\\
+  Turn off all objects:
+,0,1,0T
+  Turn on only objects with at least 50 points:
+,50,0T
+  Turn off objects with less than 100 points:
+,100,1,0T
+  Turn on only objects with at least 20 points that pass through ROI in data set "seed"
+,20,0T
+,0,1,0T
+    "seed"1,1T
+**See Also:**\\
+[[jvs:fscan|fScan Home]],
+[[jvs:fscan:manual|fScan Manual]],
+[[jvs:fscan:manual:chapter3|KeyCmds]],
+[[jvs:fscan:manual:chapter3:surfkeys|SurfKeys]],
+[[jvs:fscan:manual:help|Manual Help]]

Brain Imaging & Analysis Center

User Tools

Site Tools

Differences

Page Tools