--mov movvol

input (or output template with --inv)

--o outvol

output volume

--targ targvol

output template (or input with --inv)

--disp dispvol

displacement volume

--reg register.dat

tkRAS-to-tkRAS matrix (tkregister2 format)

--lta register.lta

Linear Transform Array (usually only 1 transform)

--fsl register.fsl

fslRAS-to-fslRAS matrix (FSL format)

--xfm register.xfm

ScannerRAS-to-ScannerRAS matrix (MNI format)

--regheader

ScannerRAS-to-ScannerRAS matrix = identity

--mni152reg

target MNI152 space (need FSL installed)

--s subject

set matrix = identity and use subject for any templates

--inv

sample from targ to mov

--tal

map to a sub FOV of MNI305 (with --reg only)

--talres resolution

set voxel size 1mm or 2mm (def is 1)

--talxfm xfmfile

default is talairach.xfm (looks in mri/transforms)

--m3z morph

non-linear morph encoded in the m3z format

--noDefM3zPath

flag indicating that the code should not be looking for the non-linear m3z morph in the default location (subj/mri/transforms), but should use the morph name as is

--inv-morph

compute and use the inverse of the m3z morph

--fstarg <vol>

optionally use vol from subject in --reg as target. default is orig.mgz

--crop scale

crop and change voxel size

--slice-crop sS eE

crop output slices to be within sS and eE

--slice-reverse

reverse order of slices, update vox2ras

--slice-bias alpha

apply half-cosine bias field

--trilin

trilinear interpolation (default)

--nearest

nearest neighbor interpolation

--cubic

cubic B-Spline interpolation

--interp interptype

interpolation cubic, trilin, nearest (default is trilin)

--mul mulval

multiply output by mulval

--precision precisionid

output precision (default is float)

--keep-precision

set output precision to that of input

--kernel

save the trilinear interpolation kernel instead

--no-resample

do not resample, just change vox2ras matrix

--rot Ax Ay Az

rotation angles (deg) to apply to reg matrix

--trans Tx Ty Tz

translation (mm) to apply to reg matrix

--shear Sxy Sxz Syz

xz is in-plane

--reg-final regfinal.dat

final reg after rot and trans (but not inv)

--synth

replace input with white Gaussian noise

--seed seed

seed for synth (default is to set from time of day)

--save-reg

write out output volume registration matrix