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jvs:fscan:manual:chapter2:roi [2015/09/19 16:32] voyvodic |
jvs:fscan:manual:chapter2:roi [2023/02/23 18:43] (current) |
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===== ROI -- Define and manipulate Regions of Interest ===== | ===== ROI -- Define and manipulate Regions of Interest ===== | ||
====usage: | ====usage: | ||
+ | [[jvs: | ||
* -roi POINT [NAME] x y z\\ | * -roi POINT [NAME] x y z\\ | ||
* -roi BLOCK [NAME] x0 y0 z0 nx ny nz\\ | * -roi BLOCK [NAME] x0 y0 z0 nx ny nz\\ | ||
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* -roi TEXT [NAME] textstring x0 y0 x1 y1 | * -roi TEXT [NAME] textstring x0 y0 x1 y1 | ||
* -roi MASK datasetname | * -roi MASK datasetname | ||
+ | * | ||
* -roi FILE roifile | * -roi FILE roifile | ||
* -roi RX refimage | * -roi RX refimage | ||
- | * -roi MEAN flag | + | * -roi AVERAGE |
+ | * -roi HEAD [NAME] flag | ||
+ | |||
+ | | ||
+ | | ||
+ | FLAG: 0 - default (bottom boundary set at top - (L/R distance) | ||
+ | 1 - | ||
+ | 010 - set intensity threshold at 10% of maxval (default is 15%) | ||
+ | 020 - set " | ||
+ | ... | ||
+ | 070 - set " | ||
+ | |||
+ | * -roi ALIGN [refimage flag refroi thisroi] | ||
+ | |||
+ | | ||
+ | to REFIMAGE dataset by scaling and translating THISROI to match REFROI. | ||
+ | | ||
+ | FLAG - option flag (default = 0) | ||
+ | | ||
+ | (default is active or first ROI) | ||
+ | | ||
+ | (default is active or first). | ||
+ | | ||
+ | |||
+ | [[jvs: | ||
* -roi CORREL flag refROI binsize corrROI name thresh | * -roi CORREL flag refROI binsize corrROI name thresh | ||
+ | |||
+ | [[jvs: | ||
* -roi CLUSTER refimage flag name | * -roi CLUSTER refimage flag name | ||
* -roi MERGE refimage flag name minvalley minsize mindist | * -roi MERGE refimage flag name minvalley minsize mindist | ||
+ | |||
+ | [[jvs: | ||
* -roi STATS refimage flag showflag mode name value nlevels level0 dlevel | * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel | ||
* -roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh | * -roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh | ||
- | [[jvs: | ||
[[jvs: | [[jvs: | ||
- | [[jvs: | ||
- | |||
- | [[jvs: | ||
- | ROI's can be added to the current data set by explicitly specifying the ROI type, location, and size. The list above shows the various ROI types and how they are specified. The meaning of he arguments is: | ||
- | * NAME - specify a name for this ROI (no spaces or punctuation) | ||
- | * X0,Y0,Z0 - specify the starting location of the ROI as upper left corner of the first slice. The default origin is 0,0,0. | ||
- | * NX,NY,NZ - specify the size of the ROI. The default size is 1x1x1 (i.e. a point) if X0,Y0,Z0 are specified, otherwise it is the entire volume. | ||
- | * RAD, | ||
- | * COLOR - specify color for ROI (24-bit RGB value) | ||
The RX type of ROI (when implemented) creates a slice prescription ROI on the current data set based on slice orientation in REFIMAGE. | The RX type of ROI (when implemented) creates a slice prescription ROI on the current data set based on slice orientation in REFIMAGE. | ||
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NAME: name of ROI list. If omitted, list is linked to | NAME: name of ROI list. If omitted, list is linked to | ||
- | input mask images. | + | input mask images. |
- | -roi MERGE refimage flag name minvalley | + | -roi MERGE refimage flag name minval |
- | The MERGE command | + | Assumes input data set is roi mask image with an ROI cluster list |
+ | (usually made with ROI CLUSTER command). | ||
+ | allows you to modify | ||
- | 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 1 - Merge adjacent clusters if: |
- | 3) smaller cluster contains fewer than MINSIZE voxels | + | 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: 2 - do not modify | + | FLAG 3 - Compare |
- | (i.e. if merging ROI clusters, change merged mask values) | + | |
| | ||
- | | + | |
- | | + | FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map) |
- | | + | FLAG 2 - REFIMAGE |
- | | + | FLAG 3 - REFIMAGE contains ROI images, typically an Atlas ROI map. |
+ | FLAG 4 - Remove clusters containing less than MINVAL voxels | ||
+ | | ||
+ | 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: | ||
+ | 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. | ||
+ | 16 - sort cluster list values by peak location (LPI -> RAS) | ||
+ | 32 - sort cluster list by cluster size (largest to smallest) | ||
+ | | ||
+ | NAME: name of ROI list. If omitted, list is linked to input mask images. | ||
+ | |||
-roi STATS refimage flag showflag mode name value nlevels level0 dlevel\\ | -roi STATS refimage flag showflag mode name value nlevels level0 dlevel\\ | ||
-roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh | -roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh | ||
- | Calulate | + | Calculate |
REFIMAGE - dataset to use as ROI mask(s) | REFIMAGE - dataset to use as ROI mask(s) | ||
FLAG - stats options (select one value 0-7; add other values) | FLAG - stats options (select one value 0-7; add other values) | ||
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NAME - save stats in file NAME, if specified | NAME - save stats in file NAME, if specified | ||
VAL: if > 0, only calculate for this mask value | VAL: if > 0, only calculate for this mask value | ||
+ | | ||
If FLAG & 02010, time-series by CYCLE, | If FLAG & 02010, time-series by CYCLE, | ||
CYCLELENG: task cycle length in secs | CYCLELENG: task cycle length in secs | ||
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LEVEL0: first threshold level (def=0) | LEVEL0: first threshold level (def=0) | ||
DLEVEL: increment between levels (def=1) | DLEVEL: increment between levels (def=1) | ||
- | If input is a Surface: | + | |
+ | | ||
FLAG | FLAG | ||
1 - surface area of AREA ROI or path length of contour ROI | 1 - surface area of AREA ROI or path length of contour ROI | ||
| | ||
- | -roi CORRELATE flag ref_roi binsize corr_roi name thresh | ||
- | |||
- | Generate new data set (named NAME) containing multiple | ||
- | correlation maps based on correlating the time course for | ||
- | each voxel within the REFROI in the current data set | ||
- | with each voxel in the CORR_ROI. The 2 ROI's can be the same; | ||
- | by default they are the entire data set volume. | ||
- | |||
- | FLAG can be used for specifying options: | ||
- | 1 - generate neighbor correlation map. Correlates each voxel time course with | ||
- | its 26 neighbors and saves the mean correlation coefficient. | ||
- | 2 - do not mask out low intensity values (by default CORRELATE assumes the -m command) | ||
- | 4 - use REFROI as CORR_ROI as well | ||
- | |||
- | REFROI can be the name of an ROI, or it can be: | ||
- | 0 - use the default: 5 if FLAG& | ||
- | 1 - use the time course at the current voxel as reference | ||
- | 2 - use the current point ROI time course as reference | ||
- | 3 - use every voxel within the current box roi as a separate reference (this generates | ||
- | 1 map per ref voxel; the ref voxel in each map will have correl value of 1.0) | ||
- | 4 - use every voxel in all active ROI's in this data set | ||
- | 5 - use every voxel in the volume | ||
- | <0 - Negative ROINUM - specify any active ROI by the negative of its ROINUM\\ | ||
- | | ||
- | Default is 3 if there is a box ROI, otherwise it is 1 | ||
- | |||
- | BINSIZE is how many voxels in each dimension to bin together | ||
- | for reference (default=1). | ||
- | |||
- | CORR_ROI is the ROI to use as a mask for which voxels to test. | ||
- | By default, | ||
- | CORR_ROI can be the name of an ROI, or it can be: | ||
- | 0 - default. same as 5 | ||
- | 1 - use REFROI as CORR_ROI | ||
- | 3 - use the current box roi as CORR_ROI | ||
- | 4 - correlate with voxels in all active ROI's in this data set | ||
- | 5 - correlate with every voxel in the data set volume (default) | ||
- | <0 - Negative ROINUM - specify any active ROI by the negative of its ROINUM | ||
- | |||
- | NAME is the name of the output data set; default adds suffix | ||
- | roicorrel to current data set name. | ||
- | |||
- | THRESH is the auto-correlation threshold for counting neighboring | ||
- | voxels as positively correlated (default=0.3) | ||
- | |||
**See Also:**\\ | **See Also:**\\ | ||
[[jvs: | [[jvs: |