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jvs:fscan:manual:chapter2:roi

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jvs:fscan:manual:chapter2:roi [2017/10/09 14:30]
voyvodic 		jvs:fscan:manual:chapter2:roi [2023/02/23 18:43] (current)
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   * -roi AVERAGE flag radiusMM thresh    * -roi AVERAGE flag radiusMM thresh 
   * -roi HEAD [NAME] flag   * -roi HEAD [NAME] flag
 +
      Create BLOCK roi by auto-detection of top, sides, & front/back of head.      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.      Arbitrarily set bottom by making I-S distance same as R-L.
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              ...              ...
           070 - set     "         "     "  70%           070 - set     "         "     "  70%
 +
   * -roi ALIGN [refimage flag refroi thisroi]   * -roi ALIGN [refimage flag refroi thisroi]
 +
      Generate affine matrix (align or wsalaign) to align current images      Generate affine matrix (align or wsalaign) to align current images
      to REFIMAGE dataset by scaling and translating THISROI to match REFROI.      to REFIMAGE dataset by scaling and translating THISROI to match REFROI.
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 [[jvs:fscan:manual:chapter2:roicorrel|Generate ROI correlations]]\\ [[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]]\\ [[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]]\\ [[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 
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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
jvs/fscan/manual/chapter2/roi.1507559415.txt.gz · Last modified: 2017/10/09 14:30 by voyvodic

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