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jvs:fscan:manual:chapter2:roi
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| Both sides previous revision Previous revision Next revision | Previous revision | ||
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jvs:fscan:manual:chapter2:roi [2017/10/09 18:38] voyvodic |
jvs:fscan:manual:chapter2:roi [2023/02/23 18:43] (current) |
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| [[jvs: | [[jvs: | ||
| * -roi CORREL flag refROI binsize corrROI name thresh | * -roi CORREL flag refROI binsize corrROI name thresh | ||
| + | |||
| [[jvs: | [[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: | [[jvs: | ||
| * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel | * -roi STATS refimage flag showflag mode name value nlevels level0 dlevel | ||
| Line 93: | Line 95: | ||
| 3) smaller cluster contains fewer than MINSIZE voxels | 3) smaller cluster contains fewer than MINSIZE voxels | ||
| FLAG 2 - Compare input cluster list to REFIMAGE cluster list. | FLAG 2 - Compare input cluster list to REFIMAGE cluster list. | ||
| + | | ||
| FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE. | FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE. | ||
| + | | ||
| REFIMAGE is the reference data set; the type of data depends on FLAG: | REFIMAGE is the reference data set; the type of data depends on FLAG: | ||
| FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map) | FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map) | ||
| Line 105: | Line 107: | ||
| | | ||
| where I starts at 1 and increments to ensure each cluster has unique index. | where I starts at 1 and increments to ensure each cluster has unique index. | ||
| + | | ||
| Other FLAG values: | Other FLAG values: | ||
| 8 - do not modify input mask image values when editting ROI list; by default | 8 - do not modify input mask image values when editting ROI list; by default | ||
| Line 112: | Line 114: | ||
| 16 - sort cluster list values by peak location (LPI -> RAS) | 16 - sort cluster list values by peak location (LPI -> RAS) | ||
| 32 - sort cluster list by cluster size (largest to smallest) | 32 - sort cluster list by cluster size (largest to 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. | ||
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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 | ||
| Line 170: | Line 172: | ||
| 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 | ||
jvs/fscan/manual/chapter2/roi.1507574286.txt.gz · Last modified: 2017/10/09 18:38 by voyvodic
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