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jvs:fscan:manual:chapter2:stability
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jvs:fscan:manual:chapter2:stability [2015/03/20 19:51] voyvodic |
jvs:fscan:manual:chapter2:stability [2023/02/23 18:43] (current) |
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| **fScan Reference Manual, Chapter 2 (CmdLineOptions): | **fScan Reference Manual, Chapter 2 (CmdLineOptions): | ||
| ===== Stability -- Calculate displacements of center-of-mass===== | ===== Stability -- Calculate displacements of center-of-mass===== | ||
| - | **usage:** -stability flag outname refimg slice maxpct | + | **usage:** -stability flag outname refimg slice maxpct |
| ===== ===== | ===== ===== | ||
| * FLAG - can take on the following values: | * FLAG - can take on the following values: | ||
| Line 8: | Line 8: | ||
| * 2 - generate dx/dy/di plots for each slice separately | * 2 - generate dx/dy/di plots for each slice separately | ||
| * 4 - censor images where dx or dy is greater than MAXPCT | * 4 - censor images where dx or dy is greater than MAXPCT | ||
| - | * 8 - print volume motion parameters | + | * 010 - print volume motion parameters |
| - | * 16 - print image motion parameters | + | * 020 - print image motion parameters |
| - | * 64 - report global X/Y motion values (mean, stdev, max) | + | * 040 - motion censor data by volume (default is by image) |
| - | * 128 - use the most frequent position as reference (otherwise use mean value) | + | * 0100 - report global X/Y motion values (mean, stdev, max) |
| - | * 512 - create a point ROI at the image center-of-mass for the central timepoint | + | * 0200 - use the most frequent position as reference (otherwise use mean value) |
| + | * 0400 - do statistics | ||
| + | * 01000 - create a point ROI at the image center-of-mass for the central timepoint | ||
| + | * 04000 - censor MAXPCT is maximum fraction of all images to censor | ||
| * 3 - generate all plots (default) | * 3 - generate all plots (default) | ||
| * REFIMG - reference time point for image registration (default=0) | * REFIMG - reference time point for image registration (default=0) | ||
| * SLICE - If specified, only that slice is done, otherwise all. | * SLICE - If specified, only that slice is done, otherwise all. | ||
| - | * MAXPCT - Used when motion censoring (FLAG & 4). Images with displacement greater than MAXPCT of a voxel will be omitted from further analysis (default MAXPCT = 25%). | + | * MAXPCT - Used when motion censoring (FLAG & 4). Images with displacement greater than MAXPCT of a voxel will be omitted from further analysis (default MAXPCT = 50% for images, 30% if censoring volumes(flag 32)). If FLAG 0400 set, displacement minimum is default (50% img/30% vol) but that threshold is increased if necessary such that no more than MAXPCT of all images are censored. |
| + | * LEVELMM - minimum motion level for reporting percent of images moved (default: 1 mm) | ||
| + | * LEVELPCT1 - (default: 5) | ||
| + | * LEVELPCT2 - (default: 20) | ||
| **See Also:**\\ | **See Also:**\\ | ||
jvs/fscan/manual/chapter2/stability.1426881085.txt.gz · Last modified: 2015/03/20 19:51 by voyvodic
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