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jvs:fscan:manual:chapter2:clusters

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jvs:fscan:manual:chapter2:clusters [2017/09/12 22:44]
voyvodic [Manipulating cluster ROIs] 		jvs:fscan:manual:chapter2:clusters [2020/07/15 15:31]
voyvodic
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 ====usage:==== ====usage:====
   * -roi CLUSTER refimage flag name   * -roi CLUSTER refimage flag name
-  * -roi MERGE refimage flag name minvalley minsize mindist+  * -roi MERGE refimage flag name minval minsize mindist
  
 ====Creating cluster ROIs==== ====Creating cluster ROIs====
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 REFIMAGE: If specified, find peak intensity values and voxel locations in REFIMAGE.\\ REFIMAGE: If specified, find peak intensity values and voxel locations in REFIMAGE.\\
 If FLAG & 1, REFIMAGE is another ROI mask data set,\\ If FLAG & 1, REFIMAGE is another ROI mask data set,\\
-iF flag & 2, REFIMAGE is another dataset with Cluster list otherwise REFIMAGE is used to find peak intensity values and voxel location.+If FLAG & 2, REFIMAGE is another dataset with Cluster list; otherwise REFIMAGE is used to find peak intensity values and voxel location.
  
 By default, ROI list is attached to input mask images.  By default, ROI list is attached to input mask images. 
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 ==== Merging Cluster ROIs ==== ==== Merging Cluster ROIs ====
--roi MERGE refimage flag name minvalley minsize mindist+-roi MERGE mode refimage flag name arg1 arg2 opflag
  
-The ROI MERGE command assumes input data set is roi mask image with an ROI cluste list +The ROI MERGE command assumes input data set is roi mask image with an ROI cluste list (usually made with ROI CLUSTER command). The ROI MERGE command allows you to modify the input data set and/or its 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 can be used in different ways (controlled by FLAG).+Merge can be used in different ways depending on the MODE.\\ 
 +  MODE is specifed by name as: 
  
-FLAG (values 1-7 specify MODE, values above 7 are flags that can be added to MODE): +  (none) - don't modify clusters themselves, just do FLAG>=8 options 
-  FLAG 1 - Merge adjacent clusters if: +  peaks  - Merge adjacent clusters if: 
-    1) distance bet peaks < MINDIST +      1) distance (in mm) bet peaks < ARG2 (default 40mm) 
-    2) stat value in valley between peaks is within MINVALLEY percent of lower peak +      2) REFIMAGE value in valley between peaks is within ARG1 percent  
-    3) smaller cluster contains fewer than MINSIZE voxels +         (default 60%) of lower peak (iff REFIMAGE specified) 
-  FLAG 2 - Compare input cluster list to REFIMAGE cluster list. +  lists 2 - Compare input cluster list to REFIMAGE cluster list. 
-   +    ARG1 is flag: 
-  FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE. +      0 - default 
-  +      1 - compare based on cluster center locs, otherwise compare peak locs  
-REFIMAGE is the reference data set; the type of data depends on FLAG: +      2 - assume cluster lists already compared (idims[7]s) 
-  FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map) +      4 - don't change cluster values for matched pairs, otherwise change  
- If REFIMAGE is omitted the VALLEY argument is ignored +          cluster values so matched clusters have same values; unmatched clusters have unique values. 
-  FLAG 2 - REFIMAGE is another mask image with attached cluster list. +      8 - remove unmatched clusters from list    
-  FLAG 3 - REFIMAGE contains ROI images, typically an Atlas ROI map. +   Matches closest clusters if distance < ARG2 (mindist) 
-  +          Sets clusters ival[7] to index of the matched cluster. 
-Other FLAG values: +          Sets vals[8] to distance between cluster peaks (or ctrs) 
-    8 - do not modify input mask image values when editting ROI list; +  map   3 - Compare input cluster list to mask ROIs in REFIMAGE. 
-        by default when ROI clusters are merged or cluster VALUEs are changed, +    If ARG1 > 0, new cluster voxel value is: 
-        the corresponding image voxel values are also changed to match the new cluster VALUEs. +      REFVALUE * ARG1 + I 
-   16 - sort cluster list values by peak location (LPI -> RAS) +        where I starts at 1 and increments to ensure each cluster has unique index. 
-   32 - sort cluster list by cluster size (largest to smallest) +    If ARG2==0, compare based on cluster center locations,  
-  +      otherwise compare peak locations. 
-NAME: name of ROI list. If omitted, list is linked to input mask images. +  small 4 - Delete clusters smaller than ARG1 size 
-  +  big   5 - Keep only ARG1 biggest clusters (delete the rest) 
-The MERGE command assumes that the current image is an ROI mask. +  pairs 6 - filter pairs based on size or distance 
- +    If ARG1==0, filter based on distance (in mm) between pair peaks 
-MERGE edits the ROI list. Merge adjacent clusters if: +    If ARG1==1, filter based on distance (in mm) between pair COMs 
-  * distance bet peaks < MINDIST\\ +    For ARG1 0/1, vals[8] for kept clusters are reset to this distance 
-  * stat value in valley between peaks is within MINVALLEY percent of lower peak\\ +    If ARG1==2, filter based on size (in voxels) of smaller in pair 
-  * smaller cluster contains fewer than MINSIZE voxels+    If ARG1==3, filter based on size (in voxels) of larger in pair 
 +    If ARG1==4, filter based on size (in voxels) summed for pair 
 +    ARG2 is minimum size/distance to keep.  Pairs that are less than the 
 +      minumum value are unpaired (cluster remain in lists) 
 +    (To remove unpaired clusters use "merge lists 0 10" in each list).
      
-FLAG: 2 - do not modify input mask image values when editting ROI list  +  REFIMAGE is the reference data set; the type of data depends on the MODE: 
-(i.e. if merging ROI clusters, change merged mask values)+    peaks - REFIMAGE is a voxel intensity map (e.g. tval map) 
 +    lists - REFIMAGE is another mask image with attached cluster list. 
 +    map  - REFIMAGE contains ROI images, typically an Atlas ROI map. 
 +    pairs - REFIMAGE is another mask image with attached cluster list. 
 +    REFIMAGE is omitted if mode is SMALL, BIG, or none.
      
-NAME: name of ROI list. If omitted, list is linked to input mask images.\\ +  As noted above, the meaning of the ARG1, ARG2 options depends on the MODE. 
-MINVALLEY: (default= 60% of lower peak maximum)\\ +   
-MINSIZE: (default= 5 voxels)\\ +  Other FLAG values: 
-MINDIST: (default= 40 mm)\\+     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. 
 +    32 - sort cluster list by cluster size (largest to smallest) 
 +    64 - sort cluster list by cluster value (smallest to largest) 
 +    96 - sort cluster list by peak magnitude 
 +   128 - sort cluster list by peak location (LPI -> RAS) 
 +  
 +  NAME: name of ROI list. If omitted, list is linked to input mask images. 
 +  MINVAL: (default= 60% of lower peak maximum)\\ 
 +  MINSIZE: (default= 5 voxels)\\ 
 +  MINDIST: (default= 40 mm)\\
      
         
jvs/fscan/manual/chapter2/clusters.txt · Last modified: 2023/02/23 18:43 (external edit)

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