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jvs:fscan:manual:chapter2:roicorrel
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jvs:fscan:manual:chapter2:roicorrel [2016/07/26 20:17] voyvodic |
jvs:fscan:manual:chapter2:roicorrel [2023/02/23 18:43] |
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| - | **fScan Reference Manual, Chapter 2 (CmdLineOptions): | ||
| - | ===== ROI -- Define and manipulate Regions of Interest ===== | ||
| - | ====usage: | ||
| - | | ||
| - | ** -roi CORRELATE | ||
| - | ** -roi CORRELATE | ||
| - | |||
| - | 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 (low 3 bits are MODE): | ||
| - | * 0 - Mode ALL: correlate every voxel in REF_ROI (seeds) with every voxel in CORR_ROI (targets) | ||
| - | * 1 - Mode LOCAL: generate neighbor correlation map. Correlates each voxel time course with its 26 neighbors and saves the mean correlation coefficient. | ||
| - | * 2 - Mode OTHER: generate inter-scan voxel correlation map. Correlates each voxel in this data set with same location in other data set. In this case REFROI is name of other data set. | ||
| - | * 4 - Mode HALF: correlate 1st half of each voxel time course w/ 2nd half | ||
| - | * 8 - include negative correlation values (usually set to 0) | ||
| - | * 16 - use REFROI as CORR_ROI as well (ignored if FLAG& | ||
| - | * 32 - do not mask out low intensity values (by default CORRELATE assumes the -m command) | ||
| - | |||
| - | REFROI specifieds the seed(s); 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 | ||
| - | * neg value - specify any active ROI by the negative of its ROINUM | ||
| - | |||
| - | Default REFROI 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). | ||
| - | |||
| - | REPEATLENG (if FLAG & 4) is the duration (secs) of the reference function -- assumes ref is repeated after this much time. Will calculate total number of REPEATLENG' | ||
| - | | ||
| - | Length of half time series to be correlated will be: | ||
| - | | ||
| - | Will correlate first half: (REFDELAY: | ||
| - | |||
| - | CORR_ROI is the ROI to use as a mask for which voxels to test. By default, | ||
| - | * 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) | ||
| - | * Neg value - specify any active ROI by the negative of its ROINUM | ||
| - | |||
| - | REFDELAY (if FLAG & 4) is the duration (secs) to ignore at beginning of data set (default = ~10s) | ||
| - | |||
| - | 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:**\\ | ||
| - | [[jvs: | ||
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jvs/fscan/manual/chapter2/roicorrel.txt · Last modified: 2023/02/23 18:43 (external edit)
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