AFNI 3D ROI Statistics (3dROIstats)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Extracts statistical summary measures from data within defined ROI masks.
Modality: 3D or 4D NIfTI/AFNI volume plus ROI mask with integer labels.
Typical Use: Extracting mean values from defined regions of interest.
Key Parameters¶
-mask (ROI mask), -nzmean (mean of non-zero voxels), -nzvoxels (count non-zero voxels), -minmax (min and max)
Key Points¶
Can handle multi-label ROI masks. Outputs one row per volume, one column per ROI.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input dataset | |
mask |
File |
Yes | Mask dataset with ROI labels | -mask |
mask_f2short |
boolean |
No | Convert float mask to short integers | -mask_f2short |
numROI |
int |
No | Assume ROIs numbered 1 to n | -numROI |
zerofill |
string |
No | Fill missing ROIs with value | -zerofill |
roisel |
File |
No | Consider only ROIs listed in selection file | -roisel |
nzmean |
boolean |
No | Mean of non-zero voxels only | -nzmean |
nzsum |
boolean |
No | Sum of non-zero voxels | -nzsum |
nzvoxels |
boolean |
No | Count non-zero voxels | -nzvoxels |
nzvolume |
boolean |
No | Volume of non-zero voxels | -nzvolume |
minmax |
boolean |
No | Min/max across all voxels | -minmax |
nzminmax |
boolean |
No | Min/max of non-zero voxels | -nzminmax |
sigma |
boolean |
No | Standard deviation (all voxels) | -sigma |
nzsigma |
boolean |
No | Standard deviation (non-zero voxels) | -nzsigma |
median |
boolean |
No | Median (all voxels) | -median |
nzmedian |
boolean |
No | Median (non-zero voxels) | -nzmedian |
summary |
boolean |
No | Output grand mean only | -summary |
mode |
boolean |
No | Mode calculation | -mode |
key |
boolean |
No | Output integer ROI identifier | -key |
quiet |
boolean |
No | Suppress column/row labels | -quiet |
nomeanout |
boolean |
No | Exclude mean column from output | -nomeanout |
oneDformat |
boolean |
No | Output as 1D format with commented labels | -1Dformat |
oneDRformat |
boolean |
No | Output as 1D format R-compatible | -1DRformat |
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 - roisel:
.1D,.txt
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
stats |
stdout |
|
log |
File |
3dROIstats.log |
Output Extensions¶
- stats:
.txt
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > ROI Analysis