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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 | + | * -roi MERGE refimage flag name minval |
====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 | ||
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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 | + | |
- | | + | |
- | + | | |
- | FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE. | + | 0 - default |
- | + | | |
- | REFIMAGE | + | 2 - assume |
- | | + | |
- | If REFIMAGE is omitted the VALLEY argument is ignored | + | |
- | FLAG 2 - REFIMAGE is another mask image with attached | + | 8 - remove unmatched clusters from list |
- | FLAG 3 - REFIMAGE contains ROI images, typically an Atlas ROI map. | + | Matches closest |
- | + | Sets clusters ival[7] | |
- | Other FLAG values: | + | Sets vals[8] to distance between |
- | 8 - do not modify input mask image values when editting ROI list; | + | |
- | by default when ROI clusters | + | |
- | the corresponding image voxel values are also changed | + | REFVALUE * ARG1 + I |
- | 16 - sort cluster | + | where I starts at 1 and increments |
- | 32 - sort cluster list by cluster size (largest | + | If ARG2==0, compare based on cluster center locations, |
- | + | | |
- | NAME: name of ROI list. If omitted, list is linked | + | small 4 - Delete clusters smaller than ARG1 size |
- | + | | |
- | The MERGE command assumes that the current image is an ROI mask. | + | |
- | + | If ARG1==0, filter based on distance (in mm) between | |
- | MERGE edits the ROI list. Merge adjacent | + | 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 |
- | * stat value in valley | + | If ARG1==2, filter based on size (in 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/ | ||
+ | minumum value are unpaired (cluster remain in lists) | ||
+ | (To remove unpaired clusters use "merge lists 0 10" in each list). | ||
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- | 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 | ||
+ | | ||
+ | pairs - REFIMAGE is another mask image with attached cluster list. | ||
+ | REFIMAGE is omitted | ||
| | ||
- | 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) | ||
+ | |||
+ | | ||
+ | | ||
+ | MINSIZE: (default= 5 voxels)\\ | ||
+ | MINDIST: (default= 40 mm)\\ | ||
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