AFNI 3D REML Fit (Improved GLM)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
GLM with ARMA(1,1) temporal autocorrelation correction using restricted maximum likelihood estimation.
Modality: 4D fMRI NIfTI/AFNI time series plus design matrix from 3dDeconvolve.
Typical Use: More accurate first-level statistics than 3dDeconvolve OLS.
Key Parameters¶
-matrix (design matrix from 3dDeconvolve -x1D), -input (4D data), -Rbuck (output stats), -Rvar (output variance)
Key Points¶
More accurate statistics than 3dDeconvolve OLS. Run after 3dDeconvolve for improved inference.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input time series dataset | -input |
matrix |
File |
Yes | Regression matrix from 3dDeconvolve (.xmat.1D file) | -matrix |
mask |
File |
No | Mask dataset | -mask |
automask |
boolean |
No | Automatically generate mask | -automask |
STATmask |
File |
No | Separate mask for FDR curve computation | -STATmask |
Rbuck |
string |
Yes | Output betas and statistics from REML | -Rbuck |
Rbeta |
string |
No | Save beta weights from REML estimation | -Rbeta |
Rvar |
string |
No | Save ARMA parameters and variance estimates | -Rvar |
Rfitts |
string |
No | Save fitted model time series | -Rfitts |
Rerrts |
string |
No | Save residuals (data minus fitted model) | -Rerrts |
Rwherr |
string |
No | Save whitened residuals | -Rwherr |
Rglt |
string |
No | Save GLT results | -Rglt |
MAXa |
double |
No | Maximum AR parameter (default 0.8, range 0.1-0.9) | -MAXa |
MAXb |
double |
No | Maximum MA parameter (default 0.8, range 0.1-0.9) | -MAXb |
Grid |
int |
No | Grid resolution for (a,b) search (default 3, range 3-7) | -Grid |
NEGcor |
boolean |
No | Allow negative correlations | -NEGcor |
ABfile |
File |
No | Read pre-estimated (a,b) parameters from dataset | -ABfile |
addbase |
File |
No | Append baseline columns from .1D file | -addbase |
slibase |
File |
No | Append slice-specific baseline regressors | -slibase |
dsort |
File |
No | Include voxel-wise baseline regressors | -dsort |
fout |
boolean |
No | Include F-statistics in bucket | -fout |
tout |
boolean |
No | Include t-statistics in bucket | -tout |
rout |
boolean |
No | Include R-squared statistics in bucket | -rout |
noFDR |
boolean |
No | Disable FDR curve computation | -noFDR |
gltsym |
string[] |
No | Define custom contrasts (symbolic GLT) | -gltsym |
GOFORIT |
boolean |
No | Force processing despite rank-deficiency warnings | -GOFORIT |
usetemp |
boolean |
No | Write intermediate data to disk (reduces RAM) | -usetemp |
verb |
boolean |
No | Enable verbose progress messages | -verb |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - matrix:
.1D,.txt - mask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - STATmask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - ABfile:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - addbase:
.1D,.txt - slibase:
.1D,.txt - dsort:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
stats |
File |
$(inputs.Rbuck)+orig.HEAD, $(inputs.Rbuck)+tlrc.HEAD |
betas |
File |
$(inputs.Rbeta)+orig.*, $(inputs.Rbeta)+tlrc.*, $(inputs.Rbeta).nii* |
variance |
File |
$(inputs.Rvar)+orig.*, $(inputs.Rvar)+tlrc.*, $(inputs.Rvar).nii* |
fitted |
File |
$(inputs.Rfitts)+orig.*, $(inputs.Rfitts)+tlrc.*, $(inputs.Rfitts).nii* |
residuals |
File |
$(inputs.Rerrts)+orig.*, $(inputs.Rerrts)+tlrc.*, $(inputs.Rerrts).nii* |
log |
File |
$(inputs.Rbuck).log |
Output Extensions¶
- stats:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - betas:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK,.nii,.nii.gz - variance:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK,.nii,.nii.gz - fitted:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK,.nii,.nii.gz - 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