++ 3dExtrema: AFNI version=AFNI_2011_12_21_1014 (Dec 16 2015) [64-bit] ++ Authored by: B. Douglas Ward This program finds local extrema (minima or maxima) of the input dataset values for each sub-brick of the input dataset. The extrema may be determined either for each volume, or for each individual slice. Only those voxels whose corresponding intensity value is greater than the user specified data threshold will be considered.
Usage: 3dExtrema options datasets where the options are:
-output pname
-quiet = Flag to suppress screen output
-nbest N Only print the first N extrema.
-sep_dist d Min. separation distance [mm] for distinct extrema
Choose type of extrema (one and only one choice):
-minima Find local minima.
-maxima [default] Find local maxima.
Choose form of binary relation (one and only one choice):
-strict [default] > for maxima, < for minima
-partial >= for maxima, <= for minima
Choose boundary criteria (one and only one choice):
-interior [default]Extrema must be interior points (not on boundary)
-closure Extrema may be boundary points
Choose domain for finding extrema (one and only one choice):
-slice [default] Each slice is considered separately
-volume The volume is considered as a whole
Choose option for merging of extrema (one and only one choice):
-remove [default] Remove all but strongest of neighboring extrema
-average Replace neighboring extrema by average
-weight Replace neighboring extrema by weighted average
Command line arguments after the above are taken to be input datasets.
- Examples:
- Compute maximum value in amygdala region of Talairach-transformed dataset
- 3dExtrema -volume -closure -sep_dist 512
- -mask_file ‘TT_Daemon::amygdala’ func_slim+tlrc’[0]’
- Show minimum voxel values not on edge of mask, where the mask >= 0.95
- 3dExtrema -minima -volume -mask_file ‘statmask+orig’
- -mask_thr 0.95 func_slim+tlrc’[0]’
- Get the maximum 3 values across the given ROI.
- 3dExtrema -volume -closure -mask_file MY_ROI+tlrc
- -nbest 3 func_slim+tlrc’[0]’
This program accepts datasets that are modified on input according to the following schemes:
‘r1+orig[3..5]’ {sub-brick selector} ‘r1+orig<100..200>’ {sub-range selector} ‘r1+orig[3..5]<100..200>’ {both selectors} ‘3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )’ {calculation}
For the gruesome details, see the output of ‘afni -help’.
++ Compile date = Dec 16 2015