NAME

bbregister

SYNOPSIS

bbregister --s <subj> --mov <volid> --reg <regfile> \
--init-<type> --<contrast>

DESCRIPTION

This program performs 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.

POSITIONAL ARGUMENTS

None

REQUIRED-FLAGGED ARGUMENTS

ArgumentExplanation
--s subjectFreeSurfer 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.datOutput FreeSurfer (tkregister-style) registration file (simple text).

Initialization Arguments (one required)

ArgumentExplanation
--init-rrInitialize using NMI as implemented in mri_robust_register.
--init-fslInitialize using FSL FLIRT (requires that FSL be installed).
--init-spmInitialize using SPM spm_coreg (requires that SPM and matlab be installed).
--init-headerAssume 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 initregfileSupply an initial registration matrix.

Contrast Arguments (one required)

ArgumentExplanation
--t1Assume t1 contrast, ie, White Matter brighter than Grey Matter
--t2Assume t2 contrast, ie, Gray Matter brighter than White Matter
--boldSame as --t2
--dtiSame as --t2

OPTIONAL-FLAGGED ARGUMENTS

ArgumentExplanation
--int intvolSupply 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-framereg to middle frame (not with --frame)
--frame framenoreg to frameno (default 0=1st)
--template-out templatesave template (good with --frame)
--o outvolresample mov and save as outvol
--s-from-reg regget subject name from regfile
--rms rmsfileRMS change in cortical surface position
--fslmat flirt.mtxoutput an FSL FLIRT matrix
--lta output.ltaoutput an LTA registration matrix (This flag can be used along with or instead of --reg!)
--lh-onlyonly use left hemi
--rh-onlyonly use right hemi
--slope1 slope1cost slope for 1st stage (default is 0.5)
--slope2 slope2cost slope for 2nd stage (default is 0.5)
--offset2 offset2cost offset for 2nd stage (default is 0)
--tol1d tol1d2nd stage 1D tolerance
--tol tol2nd stage loop tolerance (same as --tolf)
--tolf tolf2nd stage loop tolerance (same as --tol)

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

ArgumentExplanation
--nmax nPowellMaxset max number of iterations (default 36)
--rand-init randmaxrandomly change input to 1st stage reg
--gm-proj-frac fracdefault is 0.5
--gm-proj-abs absuse absolute instead of relative
--wm-proj-abs dist2nd stage, default is 2mm
--proj-abs distuse wm and gm proj abs in 2nd stage
--subsamp nsub2nd stage vertex subsampling, default is 1
--nearest2nd stage, use nearest neighbor interp (defalt is trilinear)
--epi-maskmask out brain edge and B0 regions (1st and 2nd stages)
--no-cortex-labelDo not use ?h.cortex.label to mask.
--label labelfileUse label to mask.
--brute1max maxpass 1 search -max to +max (default 4)
--brute1delta deltapass 1 search -max to +max step delta (default 4)
--subsamp1 nsubsamppass 1 vertex subsampling (default 1)
--no-pass1turn off pass 1
--surf surfnamechange surface to surfname from ?h.white
--surf-cost basenamesaves final cost as basename.?h.mgh
--surf-con basenamesaves final contrast as basename.?h.mgh
--init-reg-out outinitregsave initial reg
--initcost initcostfilesave initial cost
--spm-niiUse 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 featdirFSL 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).
--tmp tmpdirtemporary dir (implies --nocleanup)
--nocleanupdo not delete temporary files
--versionprint version and exit
--helpprint 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>