AFNI Automated Talairach Transformation (@auto_tlrc)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Automated Talairach transformation using affine registration to a template atlas.
Modality: T1-weighted 3D NIfTI/AFNI volume.
Typical Use: Legacy Talairach normalization.
Key Parameters¶
-base (template), -input (anatomical), -no_ss (skip skull strip)
Key Points¶
Legacy tool for Talairach normalization. For modern analyses, prefer @SSwarper or 3dQwarp.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input anatomical dataset | |
base |
File |
Yes | Reference template in standard space (e.g., TT_N27+tlrc) | |
suffix |
string |
No | Output dataset suffix | |
no_ss |
boolean |
No | Do not strip skull of input dataset | |
warp_orig_vol |
boolean |
No | Preserve skull in output by warping original volume | |
dxyz |
double |
No | Cubic voxel size in mm (default matches template) | |
dx |
double |
No | X voxel dimension in mm | |
dy |
double |
No | Y voxel dimension in mm | |
dz |
double |
No | Z voxel dimension in mm | |
pad_base |
double |
No | Padding in mm to prevent cropping (default 15) | |
xform |
enum |
No | Warping transformation type | |
init_xform |
File |
No | Apply preliminary affine transform before registration | |
maxite |
int |
No | Maximum iterations for alignment algorithm | |
use_3dAllineate |
boolean |
No | Use 3dAllineate instead of 3dWarpDrive | |
apar |
File |
No | Reference anatomical for applying transform | |
onewarp |
boolean |
No | Single interpolation step | |
twowarp |
boolean |
No | Dual interpolation steps | |
overwrite |
boolean |
No | Replace existing outputs |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - base:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - init_xform:
.1D,.txt - apar:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
tlrc_anat |
File |
*+tlrc.HEAD, *_at.nii, *_at.nii.gz |
transform |
File |
*.Xat.1D |
log |
File |
auto_tlrc_stdout.log |
err_log |
File |
auto_tlrc_stderr.log |
Output Extensions¶
- tlrc_anat:
+tlrc.HEAD,+tlrc.BRIK,.nii,.nii.gz - transform:
.Xat.1D
Enum Options¶
xform: affine_general, shift_rotate_scale
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Structural MRI > AFNI > Registration