AFNI 3D Linear Mixed Effects (3dLME)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Linear mixed effects modeling using R lme4 package for designs with random effects.
Modality: Subject-level 3D NIfTI/AFNI volumes with data table.
Typical Use: Longitudinal data, nested designs with random effects.
Key Parameters¶
-dataTable (input table), -model (model formula), -ranEff (random effects specification), -qVars (quantitative variables)
Key Points¶
Best for longitudinal data and nested designs. Uses R lme4 syntax. Handles missing data naturally.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
prefix |
string |
Yes | Output filename prefix | -prefix |
table |
record(lme_table_row)[] |
Yes | Data table rows (Subj, Cond, InputFile) | |
model |
string |
Yes | Fixed effects formula (e.g., cond*RT+age) | -model |
ranEff |
string |
Yes | Random effects formula (e.g., ~1 for intercept) | -ranEff |
qVars |
string |
No | Quantitative variables (comma-separated) | -qVars |
qVarCenters |
string |
No | Centering values for quantitative variables | -qVarCenters |
vVars |
string |
No | Voxel-wise covariates | -vVars |
vVarCenters |
string |
No | Centering values for voxel-wise covariates | -vVarCenters |
num_glt |
int |
No | Number of general linear t-tests | -num_glt |
gltLabel |
string[] |
No | GLT labels | -gltLabel |
gltCode |
string[] |
No | GLT coding specifications | -gltCode |
num_glf |
int |
No | Number of general linear F-tests | -num_glf |
glfLabel |
string[] |
No | GLF labels | -glfLabel |
glfCode |
string[] |
No | GLF coding specifications | -glfCode |
SS_type |
int |
No | Sum of squares type (1=sequential, 3=marginal) | -SS_type |
bounds |
string |
No | Outlier removal range (lb ub) | -bounds |
ML |
boolean |
No | Use Maximum Likelihood instead of REML | -ML |
corStr |
string |
No | Residual correlation structure formula | -corStr |
ICC |
boolean |
No | Compute intra-class correlation | -ICC |
ICCb |
boolean |
No | Bayesian ICC computation | -ICCb |
logLik |
boolean |
No | Include log-likelihood in output | -logLik |
resid |
string |
No | Output filename for residuals | -resid |
RE |
string |
No | Random effects to save | -RE |
REprefix |
string |
No | Output filename for random effects | -REprefix |
mask |
File |
No | Process voxels within mask only | -mask |
jobs |
int |
No | Number of parallel processors | -jobs |
Accepted Input Extensions¶
- table:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - mask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
stats |
File |
$(inputs.prefix)+orig.HEAD, $(inputs.prefix)+tlrc.HEAD |
residuals |
File |
$(inputs.resid)+orig.HEAD, $(inputs.resid)+tlrc.HEAD |
random_effects |
File |
$(inputs.REprefix)+orig.HEAD, $(inputs.REprefix)+tlrc.HEAD |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- stats:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - residuals:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - random_effects:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Statistical Analysis