jvs:fscan:manual:chapter2:clusters
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jvs:fscan:manual:chapter2:clusters [2015/06/06 19:31] – voyvodic | jvs:fscan:manual:chapter2:clusters [2020/07/15 15:32] – 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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It creates an ROI list (name=NAME) of clusters where each cluster is defined by its mask value. For each cluster, | 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. | store center-of-mass and radius along principal axes. | ||
- | If REFIMAGE, find peak intensity | + | |
+ | 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 | ||
By default, ROI list is attached to input mask images. | By default, ROI list is attached to input mask images. | ||
- | FLAG: (no values | + | 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 | ||
+ | * 32 - sort Cluster values by cluster size (biggest -> smallest) | ||
+ | | ||
NAME: name of ROI list. If omitted, list is linked to input mask images. | NAME: name of ROI list. If omitted, list is linked to input mask images. | ||
- | -roi MERGE refimage flag name minvalley minsize mindist | + | ==== Merging Cluster ROIs ==== |
+ | -roi MERGE mode refimage flag name arg1 arg2 opflag | ||
- | The MERGE command assumes | + | The ROI MERGE command assumes |
- | MERGE edits the ROI list. Merge adjacent clusters if: | + | Merge can be used in different ways depending on the MODE.\\ |
- | | + | |
- | * stat value in valley between peaks is within MINVALLEY percent of lower peak | + | |
- | * smaller cluster contains fewer than MINSIZE voxels | + | |
| | ||
- | FLAG: 2 - do not modify | + | (none) - don't modify clusters themselves, just do FLAG>=8 options |
- | (i.e. if merging ROI clusters, | + | peaks - Merge adjacent clusters if: |
+ | 1) distance (in mm) bet peaks < ARG2 (default 40mm) | ||
+ | 2) REFIMAGE value in valley between peaks is within ARG1 percent | ||
+ | | ||
+ | lists 2 - Compare | ||
+ | ARG1 is flag: | ||
+ | 0 - default | ||
+ | 1 - compare based on cluster center locs, otherwise compare peak locs | ||
+ | 2 - assume cluster lists already compared (idims[7]s) | ||
+ | 4 - don't change cluster | ||
+ | cluster values so matched clusters have same values; unmatched clusters have unique values. | ||
+ | 8 - remove unmatched clusters from list | ||
+ | Matches closest clusters if distance < ARG2 (mindist) | ||
+ | Sets clusters ival[7] to index of the matched cluster. | ||
+ | Sets vals[8] to distance between cluster peaks (or ctrs) | ||
+ | map 3 - Compare input cluster list to mask ROIs in REFIMAGE. | ||
+ | If ARG1 > 0, new cluster voxel value is: | ||
+ | REFVALUE * ARG1 + I | ||
+ | where I starts at 1 and increments to ensure each cluster has unique index. | ||
+ | If ARG2==0, compare based on cluster center locations, | ||
+ | otherwise compare peak locations. | ||
+ | small 4 - Delete | ||
+ | big 5 - Keep only ARG1 biggest clusters (delete the rest) | ||
+ | pairs 6 - filter pairs based on size or distance | ||
+ | If ARG1==0, filter based on distance (in mm) between pair peaks | ||
+ | If ARG1==1, filter based on distance (in mm) between pair COMs | ||
+ | For ARG1 0/1, vals[8] for kept clusters are reset to this distance | ||
+ | If ARG1==2, filter based on size (in voxels) of smaller in pair | ||
+ | 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/ | ||
+ | minumum value are unpaired (cluster remain in lists) | ||
+ | (To remove unpaired clusters use "merge lists 0 10" in each list). | ||
| | ||
- | 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 the MODE: |
- | MINVALLEY: (default= 60% of lower peak maximum)\\ | + | peaks - REFIMAGE is a voxel intensity map (e.g. tval map) |
- | MINSIZE: (default= 5 voxels)\\ | + | lists - REFIMAGE is another mask image with attached cluster list. |
- | MINDIST: (default= 40 mm)\\ | + | 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. | ||
+ | |||
+ | As noted above, the meaning of the ARG1, ARG2 options depends on the MODE. | ||
+ | |||
+ | 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. | ||
+ | 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) | ||
+ | |||
+ | | ||
+ | | ||
+ | MINSIZE: (default= 5 voxels)\\ | ||
+ | MINDIST: (default= 40 mm)\\ | ||
| | ||
**See Also:**\\ | **See Also:**\\ | ||
+ | [[jvs: | ||
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[[jvs: | [[jvs: | ||
[[jvs: | [[jvs: | ||
[[jvs: | [[jvs: | ||
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jvs/fscan/manual/chapter2/clusters.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1