AFNI 3D Resting State Functional Connectivity (3dRSFC)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Computes resting-state frequency-domain metrics including ALFF, fALFF, mALFF, and RSFA from bandpass-filtered data.
Modality: 4D resting-state fMRI NIfTI/AFNI time series plus brain mask.
Typical Use: Amplitude of low-frequency fluctuations analysis in resting-state fMRI.
Key Parameters¶
Key Points¶
Computes ALFF (amplitude of low-frequency fluctuations), fALFF (fractional ALFF), and RSFA.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 3D+time dataset | |
prefix |
string |
Yes | Output dataset prefix | -prefix |
fbot |
double |
Yes | Lowest frequency in passband (Hz) | |
ftop |
double |
Yes | Highest frequency in passband (Hz) | |
band |
string |
No | Alternative passband specification (fbot ftop) | -band |
despike |
boolean |
No | Despike each time series before processing | -despike |
nodetrend |
boolean |
No | Skip quadratic detrending before FFT | -nodetrend |
notrans |
boolean |
No | Skip initial transient checking | -notrans |
ort |
File |
No | Orthogonalize input to columns in 1D file | -ort |
dsort |
File |
No | Orthogonalize each voxel to matching voxel in dataset | -dsort |
dt |
double |
No | Set time step in seconds (default from header) | -dt |
nfft |
int |
No | FFT length | -nfft |
mask |
File |
No | Mask dataset | -mask |
automask |
boolean |
No | Create mask from input dataset | -automask |
blur |
double |
No | Blur filter width FWHM in mm | -blur |
localPV |
double |
No | Replace vectors with local principal vector (radius in mm) | -localPV |
norm |
boolean |
No | Make output time series have L2 norm = 1 | -norm |
no_rs_out |
boolean |
No | Skip time series output, calculate parameters only | -no_rs_out |
un_bp_out |
boolean |
No | Output un-bandpassed series | -un_bp_out |
no_rsfa |
boolean |
No | Skip RSFA parameter calculation | -no_rsfa |
bp_at_end |
boolean |
No | Perform bandpassing as final step | -bp_at_end |
quiet |
boolean |
No | Suppress informational messages | -quiet |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - ort:
.1D,.txt - dsort:
.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 |
|---|---|---|
filtered |
File |
$(inputs.prefix)_LFF+orig.HEAD, $(inputs.prefix)_LFF+tlrc.HEAD |
alff |
File |
$(inputs.prefix)_ALFF+orig.HEAD, $(inputs.prefix)_ALFF+tlrc.HEAD |
falff |
File |
$(inputs.prefix)_fALFF+orig.HEAD, $(inputs.prefix)_fALFF+tlrc.HEAD |
rsfa |
File |
$(inputs.prefix)_RSFA+orig.HEAD, $(inputs.prefix)_RSFA+tlrc.HEAD |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- filtered:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - alff:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - falff:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - rsfa:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Connectivity