Usage: 3dAnatNudge [options] Moves the anat dataset around to best overlap the epi dataset.
OPTIONS:
- -anat aaa = aaa is an ‘scalped’ (3dIntracranial) high-resolution
- anatomical dataset [a mandatory option]
- -epi eee = eee is an EPI dataset [a mandatory option]
- The first [0] sub-brick from each dataset is used, unless otherwise specified on the command line.
- -prefix ppp = ppp is the prefix of the output dataset;
- this dataset will differ from the input only in its name and its xyz-axes origin [default=don’t write new dataset]
- -step sss = set the step size to be sss times the voxel size
- in the anat dataset [default=1.0]
-x nx = search plus and minus nx steps along the EPI
-y ny dataset’s x-axis; similarly for ny and the
- -z nz y-axis, and for nz and the z-axis
- [default: nx=1 ny=5 nz=0]
-verb = print progress reports (this is a slow program)
NOTES *Systematically moves the anat dataset around and find the shift
that maximizes overlap between the anat dataset and the EPI dataset. No rotations are done.
is a copy of the anat, except that it’s origin will be shifted and it will have a different ID code than the anat. If you want to use this new dataset as the anatomy parent for the EPI datasets, you’ll have to use
3drefit -apar ppp+orig eee1+orig eee2+orig ...
3dbucket -fbuc -prefix epi_fb epi+orig
3dIntracranial -anat spgr+orig -prefix spgr_st
3dAnatNudge -anat spgr_st+orig -epi epi_fb+orig -prefix spgr_nudge
anat datasets spgr_st+orig and spgr_nudge+orig, to see if the nudged dataset seems like a better fit.
Delete the nudged dataset spgr_nudge.
3drefit command output by 3dAnatNudge to spgr+orig.
will be the 3drefit command string; all other messages go to stderr. This can be useful if you want to capture the command to a shell variable and then execute it, as in the following csh fragment:
set cvar = 3dAnatNudge ... if( $cvar[1] == “3drefit” ) $cvar
The test on the first sub-string in cvar allows for the possibility that the program fails, or that the optimal nudge is zero.
++ Compile date = Dec 16 2015