AFNI 3D Volume Registration (3dvolreg)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Rigid-body motion correction by registering all volumes in a 4D dataset to a base volume.
Modality: 4D fMRI NIfTI/AFNI time series.
Typical Use: Motion correction for fMRI; outputs 6 motion parameters for nuisance regression.
Key Parameters¶
-base (reference volume index or dataset), -prefix (output), -1Dfile (motion parameters output), -maxdisp1D (max displacement output)
Key Points¶
Default base is volume 0; use median volume for better results. Motion parameters output as 6 columns.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 4D dataset | |
prefix |
string |
Yes | Output dataset prefix | -prefix |
base |
int |
No | Base brick index (default 0) | -base |
base_file |
File |
No | Base brick from external dataset | -base |
interpolation |
enum |
No | Interpolation method | - |
dfile |
string |
No | Save 9-column motion parameters (roll, pitch, yaw, dS, dL, dP, rmsold, rmsnew) | -dfile |
oned_file |
string |
No | Save 6-column motion parameters for detrending | -1Dfile |
oned_matrix_save |
string |
No | Save coordinate transformation matrix | -1Dmatrix_save |
float |
boolean |
No | Force floating-point output format | -float |
clipit |
boolean |
No | Clip output values to input range (default) | -clipit |
noclip |
boolean |
No | Disable value clipping | -noclip |
maxdisp |
boolean |
No | Print max brain voxel displacement in mm | -maxdisp |
nomaxdisp |
boolean |
No | Disable max displacement calculation | -nomaxdisp |
maxdisp1D |
string |
No | Write max displacement per sub-brick to file | -maxdisp1D |
zpad |
int |
No | Zero-pad by n voxels during rotations (default 4) | -zpad |
maxite |
int |
No | Maximum iterations for convergence (default 23) | -maxite |
x_thresh |
double |
No | Convergence threshold in voxels (default 0.01) | -x_thresh |
rot_thresh |
double |
No | Rotation convergence in degrees (default 0.02) | -rot_thresh |
final |
enum |
No | Final interpolation method | -final |
weight |
File |
No | Apply voxel weighting from specified brick | -weight |
twopass |
boolean |
No | Perform two-pass registration (coarse then fine) | -twopass |
twoblur |
double |
No | Blur factor for pass 1 (default 2.0) | -twoblur |
verbose |
boolean |
No | Print progress reports | -verbose |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - base_file:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - weight:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
registered |
File |
$(inputs.prefix)+orig.HEAD, $(inputs.prefix)+tlrc.HEAD |
motion_params |
File |
$(inputs.dfile) |
motion_1D |
File |
$(inputs.oned_file) |
transform_matrix |
File |
$(inputs.oned_matrix_save) |
max_displacement |
File |
$(inputs.maxdisp1D) |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- registered:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - motion_params:
.1D - motion_1D:
.1D - transform_matrix:
.aff12.1D - max_displacement:
.1D
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Motion Correction