AFNI align_epi_anat — EPI-to-Anatomy Alignment¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Aligns EPI functional images to anatomical images with optional distortion correction using local Pearson correlation.
Modality: EPI volume (3D NIfTI) plus T1-weighted anatomical.
Typical Use: Core EPI-to-structural alignment in functional preprocessing.
Key Parameters¶
-epi (EPI dataset), -anat (anatomical), -epi_base (EPI reference volume), -cost (cost function, default lpc)
Key Points¶
lpc cost function designed for EPI-to-T1 alignment. Central tool in afni_proc.py.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
epi |
File |
Yes | EPI dataset to align | -epi |
anat |
File |
Yes | Anatomical dataset | -anat |
epi_base |
string |
Yes | EPI base used in alignment (0/mean/median/max/subbrick#) | -epi_base |
anat2epi |
boolean |
No | Align anatomical to EPI (default) | -anat2epi |
epi2anat |
boolean |
No | Align EPI to anatomical instead | -epi2anat |
suffix |
string |
No | Suffix to append to output names (default _al) | -suffix |
output_dir |
string |
No | Output directory for results | -output_dir |
big_move |
boolean |
No | Enable two-pass alignment for larger displacements | -big_move |
giant_move |
boolean |
No | Even larger movement - uses cmass, two passes, very large angles | -giant_move |
ginormous_move |
boolean |
No | Combines giant_move with center alignment | -ginormous_move |
rigid_body |
boolean |
No | Limit transformation to translation and rotation only | -rigid_body |
volreg |
enum |
No | Perform volume registration on EPI (default on) | -volreg |
tshift |
enum |
No | Enable time-series correction (default on) | -tshift |
deoblique |
enum |
No | Correct oblique dataset orientations (default on) | -deoblique |
cost |
string |
No | Alignment cost function (default lpc) | -cost |
edge |
boolean |
No | Use edge-detection method instead of standard cost | -edge |
save_all |
boolean |
No | Preserve all intermediate datasets | -save_all |
save_vr |
boolean |
No | Save motion-corrected EPI dataset | -save_vr |
save_skullstrip |
boolean |
No | Save skull-stripped anatomy | -save_skullstrip |
anat_has_skull |
enum |
No | Whether anatomical has skull | -anat_has_skull |
epi_strip |
enum |
No | Method for stripping EPI | -epi_strip |
Accepted Input Extensions¶
- epi:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - anat:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
aligned_anat |
File |
*_al+orig.HEAD, *_al+tlrc.HEAD |
aligned_epi |
File |
*_al_reg+orig.HEAD, *_al_reg+tlrc.HEAD |
transform_matrix |
File[] |
*.aff12.1D |
volreg_output |
File |
*_vr+orig.HEAD, *_vr+tlrc.HEAD |
log |
File |
align_epi_anat.log |
Output Extensions¶
- aligned_anat:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - aligned_epi:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - transform_matrix:
.aff12.1D - volreg_output:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Registration