Sorry, I have not documented it very well yet. I just added docs to our local version, so I've copied the info below:

USAGE: bbregister

Required Arguments: --s subject : FreeSurfer subject name --mov volid : input/movable volume --reg register.dat : output registration file

Initialization Arguments (one required)

--init-fsl : initialize the registration with FSL --init-spm : initialize the registration with SPM --init-header : initialize the registration based on header goemetry --init-reg initregfile : explicitly pass registration

Contrast Arguments (one required)

--t1 : assume t1 contrast, ie, WM brighter than GM --t2 : assume t2 contrast, ie, GM brighter than WM (default) --bold : same as --t2 --dti : same as --t2

Optional Arguments

--int intvol : intermediate volume --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

--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) --tol tol : 2nd stage tolerance (default is 1e-8) --rand-init randmax : randomly change input to 1st stage reg --gm-proj-frac frac : 2nd stage, default is 0.5 --wm-proj-abs dist : 2nd stage, default is 2mm --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) --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)

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

--tmp tmpdir : temporary dir (implies --nocleanup) --nocleanup : do not delete temporary files --version : print version and exit --help : print help and exit

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.

INPUTS (all required)

--s subject

Subject name as found in $SUBJECTS_DIR.

--mov movvol

"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

Output FreeSurfer (tkregister-style) registration file (simple text).

INITIALIZATION METHODS (Choose One)

--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)

--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 register.init.dat

Supply an initial registration matrix.

CONTRAST (Choose One)

There are only two types of contrast that bbregister understands: 1. Gray matter brighter than white matter (--t2, --bold, --dti) 2. White matter brighter than gray matter (--t1)

OTHER 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.

EXAMPLES:

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

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

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

Wang, Xin wrote:

Hello, Dr. Greve,

I am using bbregister to register the BOLD to T1. The --help does not provide any imformation about how it works. What are the difference from bbregister to flirt (fslregister)? more information about --intvol also needed. For example, the format of intvol.reg (.mat or .bat?) Can I reference to the help of same flag in the tkregister2?

Thank you,

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