AFNI 3D Temporal Statistics (3dTstat)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Computes voxelwise temporal statistics (mean, stdev, median, etc.) across a 4D time series.
Modality: 4D NIfTI/AFNI time series.
Typical Use: Creating mean functional images, variance maps, temporal SNR.
Key Parameters¶
-prefix (output), -mean/-stdev/-median/-max/-min (statistic type), -mask (optional mask)
Key Points¶
Default computes mean. Can compute multiple statistics in one run.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 3D+time dataset | |
prefix |
string |
Yes | Output dataset prefix | -prefix |
mean |
boolean |
No | Compute mean of input voxels | -mean |
sum |
boolean |
No | Compute sum of input voxels | -sum |
abssum |
boolean |
No | Compute absolute sum | -abssum |
sos |
boolean |
No | Compute sum of squares | -sos |
l2norm |
boolean |
No | Compute L2 norm (sqrt of sum of squares) | -l2norm |
stdev |
boolean |
No | Standard deviation (with detrending) | -stdev |
stdevNOD |
boolean |
No | Standard deviation (without detrending) | -stdevNOD |
cvar |
boolean |
No | Coefficient of variation (with detrending) | -cvar |
cvarNOD |
boolean |
No | Coefficient of variation (without detrending) | -cvarNOD |
MAD |
boolean |
No | Median absolute deviation | -MAD |
tsnr |
boolean |
No | Temporal signal-to-noise ratio | -tsnr |
min |
boolean |
No | Compute minimum | -min |
max |
boolean |
No | Compute maximum | -max |
absmax |
boolean |
No | Compute absolute maximum | -absmax |
argmin |
boolean |
No | Index of minimum | -argmin |
argmax |
boolean |
No | Index of maximum | -argmax |
median |
boolean |
No | Median of input voxels | -median |
nzmedian |
boolean |
No | Median of non-zero voxels | -nzmedian |
nzmean |
boolean |
No | Mean of non-zero voxels | -nzmean |
percentile |
double |
No | P-th percentile point | -percentile |
zcount |
boolean |
No | Count zero values | -zcount |
nzcount |
boolean |
No | Count non-zero values | -nzcount |
slope |
boolean |
No | Compute slope vs time | -slope |
autocorr |
int |
No | Autocorrelation function (first n coefficients) | -autocorr |
autoreg |
int |
No | Autoregression coefficients (first n) | -autoreg |
DW |
boolean |
No | Durbin-Watson statistic | -DW |
skewness |
boolean |
No | Measure of asymmetry | -skewness |
kurtosis |
boolean |
No | Fourth standardized moment | -kurtosis |
tdiff |
boolean |
No | Take first difference before processing | -tdiff |
datum |
enum |
No | Output data type (default float) | -datum |
nscale |
boolean |
No | Do not scale output | -nscale |
mask |
File |
No | Use as voxel mask | -mask |
mrange |
string |
No | Restrict mask values to range (a b) | -mrange |
Accepted Input Extensions¶
- input:
.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 |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- stats:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Utilities > AFNI > Image Math