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jvs:fscan:manual:chapter2:clusters [2017/09/12 23:00] voyvodic [Merging 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 | + | * -roi MERGE refimage flag name minval |
====Creating cluster ROIs==== | ====Creating cluster ROIs==== | ||
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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 | ||
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allows you to modify the input data set and/or its Cluster list. | 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): | + | |
- | | + | |
- | 1) distance bet peaks < MINDIST | + | 1) distance |
- | 2) stat value in valley between peaks is within | + | 2) REFIMAGE |
- | 3) smaller cluster contains fewer than MINSIZE voxels | + | |
- | | + | |
- | | + | ARG1 is flag: |
- | FLAG 4 - Delete clusters with size smaller than MINVALLEY voxels\\ | + | 0 - default |
- | FLAG 5 - Modify | + | 1 - compare based on cluster center locs, otherwise compare peak locs |
- | New index is: | + | 2 - assume cluster lists already compared (idims[7]s) |
- | where I starts at 1 and increments to ensure each cluster has unique index. | + | 4 - don't change cluster values for matched pairs, otherwise change |
- | | + | cluster values so matched clusters have same values; unmatched clusters have unique values. |
- | REFIMAGE is the reference data set; the type of data depends on FLAG: | + | 8 - remove unmatched clusters from list |
- | FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map) | + | Matches closest clusters if distance < ARG2 (mindist) |
- | If REFIMAGE is omitted the VALLEY argument is ignored | + | Sets clusters ival[7] to index of the matched cluster. |
- | FLAG 2 - REFIMAGE is another mask image with attached cluster list. | + | Sets vals[8] to distance between cluster peaks (or ctrs) |
- | | + | |
- | + | If ARG1 > 0, new cluster | |
- | Other FLAG values: | + | REFVALUE |
- | 8 - do not modify input mask image values when editting ROI list; | + | where I starts at 1 and increments to ensure each cluster has unique index. |
- | by default when ROI clusters are merged or cluster VALUEs are changed, | + | If ARG2==0, compare based on cluster center locations, |
- | the corresponding image voxel values are also changed to match the new cluster VALUEs. | + | |
- | 16 - sort cluster list values | + | small 4 - Delete clusters smaller than ARG1 size |
- | 32 - sort cluster list by cluster | + | 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). | ||
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+ | pairs - REFIMAGE is another mask image with attached cluster list. | ||
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+ | As noted above, the meaning of the ARG1, ARG2 options depends on the MODE. | ||
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+ | 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.\\ | + | |
- | MINVALLEY: (default= 60% of lower peak maximum)\\ | + | |
- | MINSIZE: (default= 5 voxels)\\ | + | MINSIZE: (default= 5 voxels)\\ |
- | MINDIST: (default= 40 mm)\\ | + | MINDIST: (default= 40 mm)\\ |
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