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jvs:fscan:manual:chapter3:surfkeys:objects
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jvs:fscan:manual:chapter3:surfkeys:objects [2011/11/09 19:45] voyvodic |
jvs:fscan:manual:chapter3:surfkeys:objects [2023/02/23 18:43] (current) |
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| The surface objects commands (' | The surface objects commands (' | ||
| + | |||
| + | NAME: the meaning of this argument varies depending on the MODE\\ | ||
| + | * modes 0-2: ROI mask image (default is previous window) | ||
| + | * mode 5: object param subset name | ||
| + | * mode 7: new data set name | ||
| The MODE argument controls what type of object command to perform.\\ | The MODE argument controls what type of object command to perform.\\ | ||
| MODE:\\ | MODE:\\ | ||
| - | * 0 - turn off PARAM bit(s) for fibers | + | * 0 - turn off PARAM bit(s) for objects |
| * NAME - ROI mask image (default is previous window) | * NAME - ROI mask image (default is previous window) | ||
| - | * PARAM default=1 | + | |
| + | | ||
| * FLAG: | * FLAG: | ||
| * 0 - set all objects | * 0 - set all objects | ||
| - | * 1 - VAL is ROI num if ROIs, else intensity (default) | + | * 1 - VALUE is ROI num if ROIs, else intensity (default) |
| - | * 2 - VAL is intensity value | + | * 2 - VALUE is intensity value |
| - | * 1 - turn on PARAM bit(s) for objects in ROI VALUE voxs | + | * 4 - include only objects with endpoint in ROI (default includes objects intersecting ROI) |
| - | * NAME, PARAM, and FLAG same as mode 0. | + | * 1 - turn on PARAM bit(s) for objects in ROI |
| + | * NAME, VALUE, PARAM, and FLAG same as mode 0. | ||
| * 2 - turn off PARAM for active objects not passing through ROI | * 2 - turn off PARAM for active objects not passing through ROI | ||
| - | * NAME, PARAM, and FLAG same as mode 0. | + | * NAME, VALUE, PARAM, and FLAG same as mode 0. |
| * 3 - in/activate objects based on parameter value (ObjectParam) stored with each | * 3 - in/activate objects based on parameter value (ObjectParam) stored with each | ||
| * PARAM - mask flag | * PARAM - mask flag | ||
| Line 23: | Line 30: | ||
| * >0 - in/activate where (ObjectParam & VALUE) == PARAM. | * >0 - in/activate where (ObjectParam & VALUE) == PARAM. | ||
| * FLAG - If 0 inactivate, else activate | * FLAG - If 0 inactivate, else activate | ||
| - | * 4 - in/activate objects | + | * 4 - in/activate objects |
| * PARAM - Control flag | * PARAM - Control flag | ||
| * 0 - objects with at least VALUE points | * 0 - objects with at least VALUE points | ||
| * 1 - objects with less than VALUE points | * 1 - objects with less than VALUE points | ||
| * FLAG - If 0 inactivate, else activate | * FLAG - If 0 inactivate, else activate | ||
| - | * 5 - set/clear param for tracks | + | * 5 - set/clear param for objects |
| * NAME - object param subset name | * NAME - object param subset name | ||
| * 7 - save active objects as new data set | * 7 - save active objects as new data set | ||
| * NAME - new data set name | * NAME - new data set name | ||
| - | * 8 - set OBJFLAG to ROIVALUE | + | * 8 - set OBJFLAG to VALUE |
| - | * 9 - set OBJMASK to ROIVALUE | + | * If VALUE is omitted this displays current OBJFLAG value |
| - | * Note: object parameter | + | * 9 - set OBJMASK to VALUE |
| - | * ROIVALUE | + | * If VALUE is omitted this displays current OBJMASK value |
| + | * 10 - set NUMFASTOBJECTS to VALUE | ||
| + | * If VALUE is omitted this displays current NUMFASTOBJECTS value | ||
| + | * If NUMFASTOBJECTS is positive, that many fibers will be displayed in [[jvs:fscan: | ||
| + | * 11 - generate | ||
| + | * NAME: reference image (default | ||
| + | * VALUE: | ||
| + | * 1 - FA values (1/vtx) | ||
| + | * 2 - ADC values (1/vtx) | ||
| + | * 3 - track length values (mm), 1/track | ||
| + | * 4 - length (npts) histogram of active objects | ||
| + | * 12 - generate new data set with objects as avg of all active objects connected to each ROI (1/ROI). This assumes active objects already seed selected. | ||
| + | * NAME: ROI image (default is all active objects) | ||
| + | * VALUE: Averaged values (bitmask) | ||
| + | * 1 - # of source objects (1/obj) | ||
| + | * 2 - length of tracks mm (1/obj) + StDev | ||
| + | * 4 - total average param values (1/obj) + SD | ||
| + | * 8 - average param 1/mm (1/vtx) | ||
| + | * 16 - stdev for each 1/vtx param avgs | ||
| + | * 32 - # objects along path (1/vtx) | ||
| + | * PARAM: Selection options: | ||
| + | * 1 - selected tracks connected to each ROI | ||
| + | * 2 - selected tracks connecting all pairs of ROI's (default) | ||
| + | * 4 - include tracks passing through target ROI (default is endpt in ROI) | ||
| + | * 20 - set NOBJECTS to VALUE | ||
| + | * 21 - set NCOORDS to VALUE | ||
| + | Notes:\\ | ||
| + | Track param bit 1 means track is active\\ | ||
| + | ROIVALUE - index value in ROI mask\\ | ||
| + | * 0 - all voxels | ||
| + | * >0 - voxels with value ROIVALUE | ||
| + | Examples:\\ | ||
| + | Turn off all objects: | ||
| + | 0,0,1,0T | ||
| + | Turn on only objects with at least 50 points: | ||
| + | 4,50,0T | ||
| + | Turn off objects with less than 100 points: | ||
| + | 4,100,1,0T | ||
| + | Turn on only objects with at least 20 points that pass through ROI in data set " | ||
| + | 4,20,0T | ||
| + | 0,0,1,0T | ||
| + | " | ||
| + | | ||
| **See Also:**\\ | **See Also:**\\ | ||
| [[jvs: | [[jvs: | ||
jvs/fscan/manual/chapter3/surfkeys/objects.1320867922.txt.gz · Last modified: 2014/08/04 16:03 (external edit)
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