AFNI 3D T-Test (3dttest++)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Two-sample t-test with support for covariates, paired tests, and cluster-level inference.
Modality: Subject-level 3D NIfTI/AFNI volumes.
Typical Use: Group comparisons with covariate control.
Key Parameters¶
-setA/-setB (group datasets), -prefix (output), -covariates (covariate file), -paired (paired test), -Clustsim (cluster simulation)
Key Points¶
Use -Clustsim for built-in cluster-level correction. -covariates allows continuous covariates.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
prefix |
string |
Yes | Output dataset prefix | -prefix |
setA |
File | File[] |
Yes | Primary sample set (required) | -setA |
setB |
File | File[] |
No | Secondary sample set for 2-sample comparison | -setB |
labelA |
string |
No | Name for set A in output labels | -labelA |
labelB |
string |
No | Name for set B in output labels | -labelB |
covariates |
File |
No | Text file with covariate table | -covariates |
center |
enum |
No | Covariate centering method | -center |
paired |
boolean |
No | Conduct paired-sample t-test | -paired |
unpooled |
boolean |
No | Compute variance separately for each set | -unpooled |
BminusA |
boolean |
No | Reverse subtraction order to B - A | -BminusA |
rankize |
boolean |
No | Convert data and covariates into ranks | -rankize |
toz |
boolean |
No | Convert t-statistics to z-scores | -toz |
zskip |
int |
No | Skip zero values in voxel analysis | -zskip |
resid |
string |
No | Save residuals to separate dataset | -resid |
no1sam |
boolean |
No | Omit 1-sample test results in 2-sample analysis | -no1sam |
nomeans |
boolean |
No | Exclude mean sub-bricks from output | -nomeans |
notests |
boolean |
No | Exclude statistical test sub-bricks | -notests |
mask |
File |
No | Restrict analysis to mask region | -mask |
exblur |
double |
No | Apply additional Gaussian smoothing (FWHM in mm) | -exblur |
Clustsim |
int |
No | Run cluster simulations for thresholding | -Clustsim |
ETAC |
int |
No | Multi-threshold clustering with equitable FPR control | -ETAC |
brickwise |
boolean |
No | Process multiple sub-bricks separately | -brickwise |
singletonA |
string |
No | Test single value against group mean | -singletonA |
debug |
boolean |
No | Print detailed analysis information | -debug |
Accepted Input Extensions¶
- setA:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - setB:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - covariates:
.1D,.txt - 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.*, $(inputs.resid)+tlrc.*, $(inputs.resid).nii* |
clustsim |
File |
*.ClustSim.* |
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,.nii,.nii.gz
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Statistical Analysis