AFNI 3D Mask Average (3dmaskave)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Extracts and outputs the average time series from voxels within a mask region.
Modality: 4D fMRI NIfTI/AFNI time series plus binary mask.
Typical Use: Simple ROI time series extraction for connectivity analysis.
Key Parameters¶
-mask (mask dataset), -quiet (output values only), -mrange (min max value range in mask)
Key Points¶
Simple and fast ROI time series extraction. Output is one value per timepoint to stdout.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input dataset | |
mask |
File |
No | Use mask dataset for averaging | -mask |
mindex |
int |
No | Which sub-brick from mask to use (default 0) | -mindex |
mrange |
string |
No | Restrict mask voxels to values between a and b | -mrange |
dindex |
int |
No | Select sub-brick from input dataset | -dindex |
drange |
string |
No | Include only input voxels with values between a and b | -drange |
slices |
string |
No | Restrict to slice numbers p through q | -slices |
xbox |
string |
No | Create mask using box at x y z location | -xbox |
xball |
string |
No | Create mask using sphere at x y z with radius r | -xball |
sigma |
boolean |
No | Compute standard deviation alongside mean | -sigma |
sum |
boolean |
No | Calculate sum instead of mean | -sum |
sumsq |
boolean |
No | Calculate sum of squares | -sumsq |
enorm |
boolean |
No | Calculate Euclidean norm | -enorm |
median |
boolean |
No | Calculate median instead of mean | -median |
max |
boolean |
No | Calculate maximum instead of mean | -max |
min |
boolean |
No | Calculate minimum instead of mean | -min |
perc |
int |
No | Compute the XX-th percentile value (0-100) | -perc |
dump |
boolean |
No | Print all voxel values included in result | -dump |
udump |
boolean |
No | Print unscaled voxel values | -udump |
indump |
boolean |
No | Print voxel indexes for dumped values | -indump |
quiet |
boolean |
No | Output only minimal numerical results | -quiet |
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 |
|---|---|---|
average |
stdout |
|
log |
File |
3dmaskave.log |
Output Extensions¶
- average:
.1D
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > ROI Analysis