AFNI 3D Deconvolve (GLM Analysis)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Multiple linear regression analysis for fMRI with flexible hemodynamic response function models.
Modality: 4D fMRI NIfTI/AFNI time series plus stimulus timing files.
Typical Use: First-level GLM analysis with flexible HRF models.
Key Parameters¶
-input (4D data), -polort (polynomial detrending order), -num_stimts (number of regressors), -stim_times (timing files with HRF model), -gltsym (contrasts)
Key Points¶
Supports many HRF models (GAM, BLOCK, dmBLOCK, TENT, CSPLIN). Use -x1D_stop to generate design matrix only.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 3D+time dataset | -input |
bucket |
string |
Yes | Output bucket dataset prefix | -bucket |
polort |
string |
No | Polynomial degree for baseline (default 1, 'A' for auto) | -polort |
num_stimts |
int |
No | Number of stimulus regressors | -num_stimts |
stim_times |
stim_times_spec[] |
Yes | Stimulus times specification (k tname Rmodel) | |
stim_file |
stim_file_spec[] |
Yes | Stimulus file specification (k sname) | |
stim_label |
stim_label_spec[] |
Yes | Stimulus labels (k label) | |
ortvec |
File |
No | Baseline vectors from file as nuisance regressors | -ortvec |
local_times |
boolean |
No | Interpret stimulus times relative to run starts | -local_times |
global_times |
boolean |
No | Interpret stimulus times relative to first run | -global_times |
fout |
boolean |
No | Output F-statistics for stimulus coefficients | -fout |
tout |
boolean |
No | Output t-statistics for individual coefficients | -tout |
rout |
boolean |
No | Output R-squared for each stimulus | -rout |
gltsym |
string[] |
No | General linear test symbolic specification | -gltsym |
glt_label |
record(glt_label_spec)[] |
No | GLT labels (k label) | |
x1D |
string |
No | Export design matrix filename | -x1D |
x1D_stop |
boolean |
No | Stop after matrix generation | -x1D_stop |
mask |
File |
No | Mask dataset | -mask |
automask |
boolean |
No | Automatically generate mask | -automask |
censor |
File |
No | Censor file for excluding time points | -censor |
CENSORTR |
string |
No | Censor specific TRs | -CENSORTR |
fitts |
string |
No | Output fitted model prefix | -fitts |
errts |
string |
No | Output residuals prefix | -errts |
jobs |
int |
No | Number of parallel jobs | -jobs |
quiet |
boolean |
No | Suppress progress messages | -quiet |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - stim_times:
.1D,.txt - stim_file:
.1D,.txt - ortvec:
.1D,.txt - mask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - censor:
.1D,.txt
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
stats |
File |
$(inputs.bucket)+orig.HEAD, $(inputs.bucket)+tlrc.HEAD |
design_matrix |
File |
$(inputs.x1D) |
xmat |
File |
*.xmat.1D |
fitted |
File |
$(inputs.fitts)+orig.HEAD, $(inputs.fitts)+tlrc.HEAD |
residuals |
File |
$(inputs.errts)+orig.HEAD, $(inputs.errts)+tlrc.HEAD |
log |
File |
$(inputs.bucket).log |
Output Extensions¶
- stats:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - design_matrix:
.1D - xmat:
.xmat.1D - fitted:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - residuals:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Statistical Analysis