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jvs:fscan:manual:chapter2:roi [2012/06/01 16:02] voyvodic |
jvs:fscan:manual:chapter2:roi [2023/02/23 18:43] (current) |
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**fScan Reference Manual, Chapter 2 (CmdLineOptions): | **fScan Reference Manual, Chapter 2 (CmdLineOptions): | ||
===== 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 | ||
- | ====usage for manipulating existing ROIs:==== | + | * -roi AVERAGE flag radiusMM thresh |
- | * -roi MEAN flag | + | * -roi HEAD [NAME] flag |
- | * -roi CORREL flag refname | + | |
+ | | ||
+ | | ||
+ | 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 | ||
+ | |||
+ | | ||
+ | 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 | ||
+ | |||
+ | [[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 | ||
+ | |||
+ | |||
+ | [[jvs: | ||
+ | |||
- | ====For adding new ROIs:==== | ||
- | 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. | ||
| | ||
- | -roi STATS refimage flag showflag mode name value nlevels level0 dlevel | + | 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 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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6 - include peak val& | 6 - include peak val& | ||
7 - include intensity weighted ctr loc, and above | 7 - include intensity weighted ctr loc, and above | ||
- | 010 - mean time course | + | 010 - TIMESERIES; calculate |
020 - calculate laterality index if available | 020 - calculate laterality index if available | ||
040 - calculate stats omitting zero values | 040 - calculate stats omitting zero values | ||
+ | 0100 - report ROI volumes in mm3 (voxel count X voxel volume) | ||
+ | 0200 - include ROI's with only zero values (usually ignored) | ||
+ | 0400 - WEIGHTED; weight stats by mask value | ||
+ | 01000 - no threshold | ||
+ | 02000 - CYCLES; calculate time-series stats by task cycle | ||
+ | 04000 - BINARYMASK; consider all non-zero voxels in mask as single ROI | ||
+ | |||
SHOWFLAG - Report generation flags | SHOWFLAG - Report generation flags | ||
1 - tab-separated columns in text output | 1 - tab-separated columns in text output | ||
| | ||
2 - comma-separated columns in text output | 2 - comma-separated columns in text output | ||
- | 020 - include ROI's with only zero values in report | ||
0100 - save as XML text file | 0100 - save as XML text file | ||
0200 - save as tab-delimited text file | 0200 - save as tab-delimited text file | ||
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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 | ||
- | NLVLS: # threshold levels to calc separately (def=1) | + | |
- | + | If FLAG & 02010, time-series by CYCLE, | |
- | If input is a Surface: | + | CYCLELENG: task cycle length in secs |
+ | CYCLEOFF: first cycle offset in secs (ignore images before this) | ||
+ | THRESH: mask threshold (assumes WEIGHTED and BINARYMASK) | ||
+ | otherwise, | ||
+ | | ||
+ | | ||
+ | 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 | ||
| | ||
- | |||
**See Also:**\\ | **See Also:**\\ | ||
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