• bbregister

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.

REQUIRED FLAGGED ARGUMENTS

• --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
  --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

• --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.
  --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>