FreeSurfer Boundary-Based Registration (bbregister)¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
High-quality registration of functional EPI images to FreeSurfer anatomy using white matter boundary contrast.
Modality: 3D EPI volume (mean/example func) plus FreeSurfer subject directory.
Typical Use: High-quality EPI to T1 registration using cortical surfaces.
Key Parameters¶
--s (subject), --mov (moving/source image), --reg (output registration), --init-fsl (initialization method), --bold (contrast type)
Key Points¶
Superior to volume-based registration for EPI-to-T1. Requires completed recon-all. --init-fsl recommended.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
subject |
string |
Yes | FreeSurfer subject name | --s |
source_file |
File |
Yes | Source (moveable) volume to register | --mov |
out_reg_file |
string |
Yes | Output registration file (.dat) | --reg |
contrast_type |
enum |
No | Contrast type of source image | |
init_coreg |
boolean |
No | Initialize using mri_coreg (default) | --init-coreg |
init_header |
boolean |
No | Initialize using header geometry | --init-header |
init_reg |
File |
No | Initialize with existing registration file | --init-reg |
no_coreg_ref_mask |
boolean |
No | Do not use aparc+aseg.mgz as reference mask | --no-coreg-ref-mask |
dof |
enum |
No | Degrees of freedom (6=rigid, 9=+scaling, 12=affine) | --dof |
tol |
double |
No | Second stage loop tolerance | --tol |
tol1d |
double |
No | Second stage 1D tolerance | --tol1d |
nmax |
int |
No | Max number of iterations | --nmax |
subsamp |
int |
No | Second stage vertex subsampling | --subsamp |
subsamp1 |
int |
No | Pass 1 vertex subsampling | --subsamp1 |
brute1max |
double |
No | Pass 1 brute force max translation | --brute1max |
brute1delta |
double |
No | Pass 1 brute force delta | --brute1delta |
no_brute2 |
boolean |
No | Disable brute force search on pass 2 | --no-brute2 |
lta |
boolean |
No | Output as LTA format | --lta |
fslmat |
string |
No | Output FSL-style matrix file | --fslmat |
int |
File |
No | Intermediate volume for registration | --int |
mid_frame |
boolean |
No | Use middle frame of source | --mid-frame |
frame |
int |
No | Use specific frame of source (0-based) | --frame |
fsl_bet_mov |
boolean |
No | Apply BET to moveable volume | --fsl-bet-mov |
no_fsl_bet_mov |
boolean |
No | Do not apply BET to moveable volume | --no-fsl-bet-mov |
tmp |
string |
No | Temporary directory | --tmp |
nocleanup |
boolean |
No | Do not delete temporary files | --nocleanup |
Accepted Input Extensions¶
- source_file:
.mgz,.mgh,.nii,.nii.gz - init_reg:
.dat,.lta - int:
.mgz,.mgh,.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
out_reg |
File |
$(inputs.out_reg_file) |
out_fsl_mat |
File |
$(inputs.fslmat) |
mincost |
File |
*.mincost |
log |
File |
bbregister.log |
Output Extensions¶
- out_reg:
.dat,.lta - out_fsl_mat:
.mat - mincost:
.mincost
Enum Options¶
contrast_type: t1, t2, bold, dti
init: coreg, rr, spm, fsl, header, best
dof: 6, 9, 12
Docker Tags¶
Available versions: latest, 8.1.0, 8.0.0, 7.2.0, 7.3.0, 7.3.1, 7.3.2, 7.4.1, 7.1.1, 6.0
Categories¶
- Functional MRI > FreeSurfer > Functional Analysis