FSL Mean Time Series Extraction (fslmeants)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Extracts the mean time series from a 4D dataset within a mask or at specified coordinates.
Modality: 4D fMRI NIfTI time series plus ROI mask or coordinates.
Typical Use: ROI time series extraction for seed-based connectivity analysis.
Key Parameters¶
-i (input 4D), -o (output text file), -m (mask image), -c (x y z coordinates), --eig (output eigenvariates)
Key Points¶
Outputs one value per timepoint. Use -m for mask-based extraction, -c for single-voxel. --eig outputs eigenvariate (first principal component) instead of mean.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 4D image | -i |
output |
string |
Yes | Output text file for timeseries | -o |
mask |
File |
No | Mask image | -m |
label |
File |
No | Label image for extracting timeseries per label | --label= |
coord |
string |
No | Voxel coordinates (x y z) for single voxel timeseries | -c |
usemm |
boolean |
No | Use mm coordinates instead of voxel coordinates | --usemm |
showall |
boolean |
No | Show all voxel time series instead of mean | --showall |
transpose |
boolean |
No | Output in transposed format (time x voxels) | --transpose |
eig |
boolean |
No | Calculate eigenvariates instead of mean | --eig |
order |
int |
No | Number of eigenvariates to output | --order= |
nobin |
boolean |
No | Do not binarize mask for eigenvariate calculation | --no_bin |
verbose |
boolean |
No | Enable verbose output | -v |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - mask:
.nii,.nii.gz - label:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
timeseries |
File |
$(inputs.output) |
log |
File |
fslmeants.log |
Output Extensions¶
- timeseries:
.txt
Docker Tags¶
Available versions: latest, 6.0.4-patched2, 6.0.4-patched, 6.0.4, 6.0.4-xenial, 5.0.11, 6.0.0, 6.0.1, 5.0.9
Categories¶
- Utilities > FSL > Image Math