bbregister is a program to perform within-subject, cross-modal registration using a
boundary-based cost function. The registration is constrained to be 6 
DOF (rigid). It is required that you have an anatomical scan of the 
subject that has been analyzed in freesurfer.  Those using bbregister should site: Greve, D. N., and Fischl, B. (2009). "Accurate and robust brain image alignment using boundary-basedregistration." Neuroimage, 48, 63-72. <<BR>>

REQUIRED FLAGGED ARGUMENTS <<BR>>
        --s subject
                FreeSurfer subject name as found in $SUBJECTS_DIR.

        --mov volid
                "Moveable" volume. This is the template for the cross-modal 
                volume. Eg, for fMRI, it is the volume used for motion 
                correction.

        --reg register.{dat,lta}
                Output FreeSurfer registration file (tkregister-style or LTA 
                format).

        --vsm VoxelShiftMap 
                Include B0 distortion correction while performing 
                registration. A voxel shift map can be created from a B0 map 
                with the epidewarp.fsl script (in FreeSurfer)

        Initialization Arguments<<BR>>

        --init-coreg (Default)
                Initialize the FreeSurfer mri_coreg program.

        --no-coreg-ref-mask
                Do NOT use aparc+aseg.mgz as a reference mask. It will not 
                attempt to use aparc+aseg if it is not there. 
        --init-header
                Assume that the geometry information in the cross-modal and 
                anatomical are sufficient to get a close voxel-to-voxel 
                registration. This usually is only the case if they were 
                acquired in the same session.

        --init-reg initregfile
                Supply an initial registration matrix; can be LTA.

        Contrast Arguments (one required)

        --t1
                Assume t1 contrast, ie, White Matter brighter than Grey Matter

        --t2
                Assume t2 contrast, ie, Gray Matter brighter than White Matter

        --bold
                Same as --t2

        --dti
                Same as --t2

OPTIONAL FLAGGED ARGUMENTS <<BR>>
        --int intvol
                Supply a volume to use an an intermediate volume when 
                performing registration. This is useful for when the 
                cross-modal is volume is a partial field-of-view (FoV). If you
                acquire in the same session a whole-head FoV, then pass the 
                whole-head as the intermediate and the partial as the 
                moveable.

        --mid-frame
                reg to middle frame (not with --frame)

        --frame frameno
                reg to frameno (default 0=1st)

        --template-out template
                save template (good with --frame)

        --o outvol
                resample mov and save as outvol

        --s-from-reg reg
            get subject name from regfile

        --rms rmsfile
                RMS change in cortical surface position

        --fslmat flirt.mtx
                output an FSL FLIRT matrix

        --lta output.lta
                output an LTA registration matrix (This flag can be used along
                with or instead of --reg!) 

        --lh-only
                only use left hemi

        --rh-only
                only use right hemi

        --slope1 slope1
                cost slope for 1st stage (default is 0.5)

        --slope2  slope2
                cost slope for 2nd stage (default is 0.5)

        --offset2 offset2
                cost offset for 2nd stage (default is 0)

        --tol1d tol1d
                2nd stage 1D tolerance 

        --tol tol
                2nd stage loop tolerance (same as --tolf)

        --tolf  tolf
                2nd stage loop tolerance (same as --tol)

        Be careful making these more stringent as they can cause underflows 
        and NaNs.<<BR>>

        --nmax nPowellMax
                set max number of iterations (default 36)

        --rand-init randmax
                randomly change input to 1st stage reg
        --gm-proj-frac frac
                default is 0.5

        --gm-proj-abs abs
                use absolute instead of relative

        --wm-proj-abs  dist
                2nd stage, default is 2mm

        --proj-abs  dist
                use wm and gm proj abs in 2nd stage

        --subsamp nsub
                2nd stage vertex subsampling, default is 1

        --nearest
                2nd stage, use nearest neighbor interp (defalt is trilinear)

        --epi-mask
                mask out brain edge and B0 regions (1st and 2nd stages)

        --no-cortex-label
                Do not use ?h.cortex.label to mask. 

        --label labelfile
                Use label to mask. Only vertices in the label are used.

        --brute1max max
                pass 1 search -max to +max (default 4)

        --brute1delta delta
                pass 1 search -max to +max step delta (default 4)

        --subsamp1 nsubsamp
                pass 1 vertex subsampling (default 1)

        --no-pass1
                turn off pass 1

        --no-brute2
                turn off brute force search on pass 2

        --surf surfname
                change surface to surfname from ?h.white 
        --surf-cost basename
                saves final cost as basename.?h.mgh

        --surf-con  basename
                saves final contrast as basename.?h.mgh

        --init-surf-cost basename
                saves initial cost as basename.?h.mgh

        --init-reg-out outinitreg
                save initial reg

        --initcost initcostfile
                save initial cost

        --cost-fail costvalue
                exit with error if the final cost exceeds costvalue 

        --12, --9, --6
                Use 12 or 9 or 6 DOF (6 is default)

        --coreg-dof coregDOF
                Set dof to use for mri_coreg

        --spm-nii
                Use NIFTI format as input to SPM when using --init-spm 
                (spmregister). Ordinarily, it uses ANALYZE images to be 
                compatible with older versions of SPM, but this has caused 
                some left-right reversals in SPM8.

        --feat featdir
                FSL FEAT directory. Sets mov to featdir/example_func, uses 
                --init-fsl, --bold, sets reg to featdir/reg/freesurfer/
                anat2exf.register.dat. This replaces reg-feat2anat.

        --fsl-bet-mov
                When using FSL, apply BET to mov volume (turned by default).

        --init-rr
                Initialize using NMI as implemented in mri_robust_register.

        --init-fsl
                Initialize using FSL FLIRT (requires that FSL be installed).

        --init-spm
                Initialize using SPM spm_coreg (requires that SPM and matlab 
                be installed).

        --tmp tmpdir
                temporary dir (implies --nocleanup)

        --nocleanup
                do not delete temporary files

        --version
                print version and exit

        --help
                print help and exit

EXAMPLE 1
        Intialize with FLIRT, view result with tkregister2:
        bbregister --s bert --mov func.nii --init-fsl --reg 
        register.dat
        tkregister2 --mov func.nii --reg register.dat --surf 

EXAMPLE 2
        Intialize with SPM, view result with tkregister2:
        bbregister --s bert --mov func.nii --init-spm --reg 
        register.dat
        tkregister2 --mov func.nii --reg register.dat --surf

EXAMPLE 3
        Register a partial FoV using whole FoV as intermdediate:
        bbregister --s bert --mov partial.nii --init-fsl --int whole.nii --reg
        register.partial.dat
        tkregister2 --mov partial.nii --reg register.partial.dat --surf

REPORTING
        Report bugs to <freesurfer@nmr.mgh.harvard.edu>