--mov movvol

Source volume

--ref refvol

Target volume (can use --targ also)

--reg reg.lta

Output registration (can 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

--linmintol linmintol

Default is 1.000e-03

--sat SatPct

Saturation threshold, default is 9.999+01

--conf-ref

Conform the reference without rescaling (good for gca)

--no-bf

Do not do brute force search

--bf-lim lim

Constrain brute force search to +/- lim

--bf-nsamp nsamples

Number of samples in brute force search

--no-smooth

Do not apply smoothing to either ref or mov

--ref-fwhm fwhm

Apply smoothing to ref

--mov-oob

Count mov voxels that are out-of-bounds as 0

--no-mov-oob

Do not count mov voxels that are out-of-bounds as 0 (default)

--mat2par reg.lta

Extract parameters out of registration

--debug

Turn on debugging

--checkopts

Do not run anything, just check options and exit

--help

Print out information on how to use this program

--version

Print out version and exit