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jvs:fscan:manual:chapter2:roi [2016/07/26 19:57]
voyvodic 		jvs:fscan:manual:chapter2:roi [2023/02/23 18:43] (current)
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 ===== ROI -- Define and manipulate Regions of Interest ===== ===== ROI -- Define and manipulate Regions of Interest =====
 ====usage:==== ====usage:====
 +[[jvs:fscan:manual:chapter2:addroi|Adding new ROIs]]\\
   * -roi POINT [NAME] x y z\\   * -roi POINT [NAME] x y z\\
   * -roi BLOCK [NAME] x0 y0 z0 nx ny nz\\   * -roi BLOCK [NAME] x0 y0 z0 nx ny nz\\
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   * -roi TEXT [NAME] textstring x0 y0 x1 y1   * -roi TEXT [NAME] textstring x0 y0 x1 y1
   * -roi MASK datasetname   * -roi MASK datasetname
 +  * 
   * -roi FILE roifile   * -roi FILE roifile
   * -roi RX refimage  (not yet implemented)   * -roi RX refimage  (not yet implemented)
-  * -roi MEAN flag+  * -roi AVERAGE flag radiusMM thresh  
 +  * -roi HEAD [NAME] flag 
 + 
 +     Create BLOCK roi by auto-detection of top, sides, & front/back of head. 
 +     Arbitrarily set bottom by making I-S distance same as R-L. 
 +      FLAG: 0 - default (bottom boundary set at top - (L/R distance) 
 +            1 -  
 +          010 - set intensity threshold at 10% of maxval (default is 15%) 
 +          020 - set     "         "     "  20% 
 +             ... 
 +          070 - set     "         "     "  70% 
 + 
 +  * -roi ALIGN [refimage flag refroi thisroi] 
 + 
 +     Generate affine matrix (align or wsalaign) to align current images 
 +     to REFIMAGE dataset by scaling and translating THISROI to match REFROI. 
 +       REFIMAGE - data set to align to (prevwin by default) 
 +       FLAG - option flag (default = 0) 
 +       REFROI - name or ROINUM for REFIMAGE roi to use 
 +                (default is active or first ROI) 
 +       THISROI - name or ROINUM for current image roi 
 +                (default is active or first). 
 +     Example usage is to align head rois (see: -roi HEAD) 
 + 
 +[[jvs:fscan:manual:chapter2:roicorrel|Generate ROI correlations]]\\
   * -roi CORREL flag refROI binsize corrROI name thresh   * -roi CORREL flag refROI binsize corrROI name thresh
 +
 +[[jvs:fscan:manual:chapter2:clusters|Cluster ROIs]]\\
   * -roi CLUSTER refimage flag name   * -roi CLUSTER refimage flag name
   * -roi MERGE refimage flag name minvalley minsize mindist   * -roi MERGE refimage flag name minvalley minsize mindist
 +
 +[[jvs:fscan:manual:chapter2:roistats|Generate ROI statistics]]\\
   * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel    * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel 
   * -roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh    * -roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh 
  
-[[jvs:fscan:manual:chapter2:addroi|Adding new ROIs]] 
  
 [[jvs:fscan:manual:chapter2:editroi|Modifying ROIs]] [[jvs:fscan:manual:chapter2:editroi|Modifying ROIs]]
  
-[[jvs:fscan:manual:chapter2:clusters|Cluster ROIs]] 
- 
-[[jvs:fscan:manual:chapter2:roistats|Generate ROI statistics]] 
- 
-[[jvs:fscan:manual:chapter2:roicorrel|Generate ROI correlations]] 
  
-ROI's can be added to the current data set by explicitly specifying the ROI type, location, and size. The list above shows the various ROI types and how they are specified. The meaning of he arguments is: 
-  * NAME - specify a name for this ROI (no spaces or punctuation) 
-  * X0,Y0,Z0 - specify the starting location of the ROI as upper left corner of the first slice. The default origin is 0,0,0. 
-  * NX,NY,NZ - specify the size of the ROI. The default size is 1x1x1 (i.e. a point) if X0,Y0,Z0 are specified, otherwise it is the entire volume. 
-  * RAD,RADX,RADY,RADZ - specify radii for circular ROIs 
-  * COLOR - specify color for ROI (24-bit RGB value) 
  
 The RX type of ROI (when implemented) creates a slice prescription ROI on the current data set based on slice orientation in REFIMAGE. The RX type of ROI (when implemented) creates a slice prescription ROI on the current data set based on slice orientation in REFIMAGE.
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  NAME: name of ROI list. If omitted, list is linked to   NAME: name of ROI list. If omitted, list is linked to 
-          input mask images.+          input mask images.  
  
--roi MERGE refimage flag name minvalley minsize mindist+-roi MERGE refimage flag name minval minsize mindist
  
-The MERGE command assumes that the current image is an ROI mask.+Assumes input data set is roi mask image with an ROI cluster list 
 +(usually made with ROI CLUSTER command). The ROI MERGE command 
 +allows you to modify the input data set and/or its Cluster list.
  
-MERGE edits the ROI list. Merge adjacent clusters if: +Merge can be used in different ways (controlled by FLAG): 
-  1) distance bet peaks < MINDIST  + 
-  2) stat value in valley between peaks is within MINVALLEY percent of lower peak +  FLAG 1 - Merge adjacent clusters if:  
-  3) smaller cluster contains fewer than MINSIZE voxels+    1) distance bet peaks < MINDIST 
 +    2) stat value in valley between peaks is within MINVAL percent of lower peak 
 +    3) smaller cluster contains fewer than MINSIZE voxels 
 +  FLAG 2 - Compare input cluster list to REFIMAGE cluster list.
      
-  FLAG: 2 - do not modify input mask image values when editting ROI list +  FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE.
-   (i.e. if merging ROI clusters, change merged mask values)+
      
-  NAME: name of ROI list. If omitted, list is linked to input mask images. +  REFIMAGE is the reference data set; the type of data depends on FLAG: 
-  MINVALLEY: (default= 60% of lower peak maximum) +    FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map) 
-  MINSIZE: (default= 5 voxels) +    FLAG 2 - REFIMAGE is another mask image with attached cluster list. 
-  MINDIST: (default= 40 mm)+    FLAG 3 - REFIMAGE contains ROI images, typically an Atlas ROI map. 
 +    FLAG 4 - Remove clusters containing less than MINVAL voxels 
 +    FLAG 5 - Use REFIMAGE to adjust cluster index values. For each cluster, find 
 +             REFIMAGE mask value (REFVALUE) at cluster center. New cluster index is: 
 +                     REFVALUE * MINVAL + I 
 +             where I starts at 1 and increments to ensure each cluster has unique index.
      
 +  Other FLAG values:
 +    8 - do not modify input mask image values when editting ROI list; by default
 +        when ROI clusters are merged or cluster VALUEs are changed, the corresponding 
 +        image voxel values are also changed to match the new cluster VALUEs.
 +   16 - sort cluster list values by peak location (LPI -> RAS)
 +   32 - sort cluster list by cluster size (largest to smallest)
 +  
 +  NAME: name of ROI list. If omitted, list is linked to input mask images.
 +
 -roi STATS refimage flag showflag mode name value nlevels level0 dlevel\\ -roi STATS refimage flag showflag mode name value nlevels level0 dlevel\\
 -roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh  (if flag TIMESERIES) -roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh  (if flag TIMESERIES)
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   NAME - save stats in file NAME, if specified   NAME - save stats in file NAME, if specified
   VAL: if > 0, only calculate for this mask value   VAL: if > 0, only calculate for this mask value
 +  
   If FLAG & 02010, time-series by CYCLE,     If FLAG & 02010, time-series by CYCLE,  
     CYCLELENG: task cycle length in secs     CYCLELENG: task cycle length in secs
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     LEVEL0: first threshold level (def=0)     LEVEL0: first threshold level (def=0)
     DLEVEL: increment between levels (def=1)     DLEVEL: increment between levels (def=1)
-If input is a Surface:+   
 +  If input is a Surface:
   FLAG   FLAG
     1 - surface area of AREA ROI or path length of contour ROI     1 - surface area of AREA ROI or path length of contour ROI
          
- 
 **See Also:**\\ **See Also:**\\
 [[jvs:fscan:manual:chapter2:addroi|Create ROIs]], [[jvs:fscan:manual:chapter2:addroi|Create ROIs]],
jvs/fscan/manual/chapter2/roi.1469563062.txt.gz · Last modified: 2016/07/26 19:57 by voyvodic

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