--mov movvol

Source volume

--ref refvol

Target volume (can use --targ also)

--reg reg.lta

Output registration (cause use --lta too_)

--s subject

forces --ref-mask aparc+aseg.mgz

--dof DOF

Default is 6 (also: --6, --9, --12)

--ref-mask refmaskvol

Mask ref with refmaskvol

--no-ref-mask

Do not mask ref (good to undo aparc+aseg.mgz, put AFTER --s)

--mov-mask movmaskvol

Mask ref with movmaskvol

--threads nthreads

--sd SUBJECTS_DIR

--regdat reg.dat

--no-coord-dither

Turn off coordinate dithering

--no-intensity-dither

Turn off intensity dithering

--sep voxsep1 <--sep voxsep2>

Set spatial scales (def is 2 vox and 4 vox)

--trans Tx Ty Tz

Initial translation in mm (implies --no-cras0)

--rot Rx Ry Rz

Initial rotation in deg

--shear Hxy Hxz Hyz

Initial shear

--params outparamfile

Save parameters in this file

--no-cras0

Do not set translation parameters to align centers of mov and ref

--regheader

Same as no-cras0

--nitersmax n

Default is 4

--ftol ftol

Default is 1.000e-07