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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