jvs:fscan:manual:chapter2:clusters
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jvs:fscan:manual:chapter2:clusters [2015/06/06 19:29] – created voyvodic | jvs:fscan:manual:chapter2:clusters [2017/12/08 18:11] – voyvodic | ||
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====usage: | ====usage: | ||
* -roi CLUSTER refimage flag name | * -roi CLUSTER refimage flag name | ||
- | * -roi MERGE refimage flag name minvalley | + | * -roi MERGE refimage flag name minval |
- | * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel | + | |
====Creating cluster ROIs==== | ====Creating cluster ROIs==== | ||
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-roi CLUSTER refimage flag name | -roi CLUSTER refimage flag name | ||
- | Assumes | + | |
- | Create | + | This assumes |
- | | + | It creates |
- | | + | store center-of-mass and radius along principal axes. |
- | If REFIMAGE, find peak intensity value and voxel location. | + | |
- | By default, ROI list is attached to input mask images. | + | |
- | FLAG: (no values yet) | + | |
- | + | ||
- | NAME: name of ROI list. If omitted, list is linked to | + | |
- | input mask images. | + | |
+ | REFIMAGE: If specified, find peak intensity values and voxel locations in REFIMAGE.\\ | ||
+ | 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. | ||
+ | |||
+ | By default, ROI list is attached to input mask images. | ||
+ | |||
+ | FLAG (values 1-7 specify MODE, values above 7 are flags that can be added to MODE): | ||
+ | |||
+ | * 1 - create a new cluster list; 1 cluster for each group of contiguous voxels\\ | ||
+ | * 2 - compare 2 cluster lists\\ | ||
+ | * 8 - assign cluster ROIs new VALUEs based on REFIMAGE ROIs. For each cluster ROI with peak/center inside a REF ROI, the new cluster ROI value is:\\ | ||
+ | | ||
+ | For multiple cluster ROIs within the same REF ROI, the Clus_within_REF_num is assigned a value 0-9. | ||
+ | If(FLAG& | ||
+ | * 16 - sort Cluster values | ||
+ | * 32 - sort Cluster values by cluster size (biggest -> smallest) | ||
+ | | ||
+ | NAME: name of ROI list. If omitted, list is linked to input mask images. | ||
+ | |||
+ | ==== Merging Cluster ROIs ==== | ||
-roi MERGE refimage flag name minvalley minsize mindist | -roi MERGE refimage flag name minvalley minsize mindist | ||
- | The MERGE command assumes | + | The ROI MERGE command assumes |
+ | (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 | + | FLAG (values 1-7 specify MODE, values above 7 are flags that can be added to MODE): |
- | 3) smaller cluster contains fewer than MINSIZE voxels | + | FLAG 1 - Merge adjacent clusters if: |
+ | 1) distance bet peaks < MINDIST | ||
+ | 2) stat value in valley between peaks is within | ||
+ | 3) smaller cluster contains fewer than MINSIZE voxels | ||
+ | FLAG 2 - Compare input cluster list to REFIMAGE cluster list. | ||
+ | FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE. | ||
+ | FLAG 4 - Delete clusters with size smaller than MINVAL voxels | ||
+ | FLAG 5 - Modify cluster index based on REFIMAGE mask | ||
+ | New index is: REFMASKVALUE * MINVAL + I | ||
+ | where I starts at 1 and increments to ensure each cluster has unique index. | ||
+ | |||
+ | REFIMAGE is the reference data set; the type of data depends on FLAG: | ||
+ | FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map) | ||
+ | FLAG 2 - REFIMAGE is another mask image with attached cluster list. | ||
+ | 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: | ||
+ | | ||
+ | where I starts at 1 and increments to ensure each cluster has unique index. | ||
| | ||
- | | + | Other FLAG values: |
- | (i.e. if merging | + | 8 - do not modify input mask image values when editting ROI list; |
- | + | by default when ROI clusters | |
- | NAME: name of ROI list. If omitted, list is linked to input mask images. | + | the corresponding image voxel values |
- | | + | 16 - sort cluster list values by peak location (LPI -> RAS) |
- | MINSIZE: (default= 5 voxels) | + | 32 - sort cluster list by cluster size (largest to smallest) |
- | MINDIST: (default= 40 mm) | + | |
+ | 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)\\ | ||
| | ||
**See Also:**\\ | **See Also:**\\ | ||
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jvs/fscan/manual/chapter2/clusters.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1