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jvs:fscan:manual:chapter2:clusters
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jvs:fscan:manual:chapter2:clusters [2017/09/12 22:38] voyvodic |
jvs:fscan:manual:chapter2:clusters [2023/02/23 18:43] |
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| - | **fScan Reference Manual, Chapter 2 (CmdLineOptions): | ||
| - | ===== ROI -- Define and manipulate Cluster Regions of Interest ===== | ||
| - | ====usage: | ||
| - | * -roi CLUSTER refimage flag name | ||
| - | * -roi MERGE refimage flag name minvalley minsize mindist | ||
| - | ====Creating cluster ROIs==== | ||
| - | The CLUSTER type ROI assumes that the current data set is an ROI mask image (in which regions are defined by voxels with the same intensity value). The CLUSTER command uses the input mask image to create an ROI list (name=NAME) of CLUSTER type ROIs where each cluster is defined by its mask value. For each CLUSTER, the center-of-mass location and the radius along the 3 principal axes are stored. By default, the new ROI list is attached to the input mask data set. | ||
| - | * REFIMAGE, find peak intensity value and voxel location. | ||
| - | * FLAG: (no values yet) | ||
| - | * NAME: name of ROI list. If omitted, the list is linked to input mask images. | ||
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| - | ====Manipulating cluster ROIs==== | ||
| - | The ROI command can also be used to manipulate existing ROI's. | ||
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| - | -roi CLUSTER refimage flag name | ||
| - | |||
| - | This assumes roi mask image as input. | ||
| - | It creates an ROI list (name=NAME) of clusters where each cluster is defined by its mask value. For each cluster, | ||
| - | store center-of-mass and radius along principal axes. | ||
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| - | 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. | ||
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| - | By default, ROI list is attached to input mask images. | ||
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| - | FLAG (values 1-7 specify MODE, values above 7 are flags that can be added to MODE): | ||
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| - | * 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. | ||
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| - | -roi MERGE refimage flag name minvalley minsize mindist | ||
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| - | The MERGE command assumes that the current image is an ROI mask. | ||
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| - | MERGE edits the ROI list. Merge adjacent clusters if: | ||
| - | * distance bet peaks < MINDIST\\ | ||
| - | * stat value in valley between peaks is within MINVALLEY percent of lower peak\\ | ||
| - | * smaller cluster contains fewer than MINSIZE voxels | ||
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| - | FLAG: 2 - do not modify input mask image values when editting ROI list | ||
| - | (i.e. if merging ROI clusters, change merged mask values) | ||
| - | | ||
| - | NAME: name of ROI list. If omitted, list is linked to input mask images.\\ | ||
| - | MINVALLEY: (default= 60% of lower peak maximum)\\ | ||
| - | MINSIZE: (default= 5 voxels)\\ | ||
| - | MINDIST: (default= 40 mm)\\ | ||
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| - | **See Also:**\\ | ||
| - | [[jvs: | ||
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jvs/fscan/manual/chapter2/clusters.txt · Last modified: 2023/02/23 18:43 (external edit)
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