SIENA Cross-Sectional (SIENAX)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Multi-step pipeline for cross-sectional brain volume estimation. Internally chains BET brain extraction, atlas registration, FAST tissue segmentation, and head-size-normalized volume computation.
Modality: T1-weighted 3D NIfTI volume.
Typical Use: Single timepoint normalized brain volume measures.
Key Parameters¶
-o (output directory), -r (regional analysis), -BET (BET options), -S (SIENAX options)
Key Points¶
Single timepoint analysis. Normalizes volumes by head size for cross-subject comparisons. Reports total brain, GM, and WM volumes.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input T1-weighted image | |
output_dir |
string |
No | Output directory name | -o |
bet_options |
string |
No | BET options (e.g., "-f 0.3") | -B |
two_class |
boolean |
No | Two-class segmentation (no grey/white separation) | -2 |
t2_weighted |
boolean |
No | Input is T2-weighted | -t2 |
regional |
boolean |
No | Estimate regional volumes (peripheral GM, ventricular CSF) | -r |
lesion_mask |
File |
No | Lesion mask to correct mislabeled GM voxels | -lm |
fast_options |
string |
No | FAST segmentation options (e.g., "-i 20") | -S |
top_threshold |
double |
No | Ignore from this height (mm) upwards in MNI space | -t |
bottom_threshold |
double |
No | Ignore from this height (mm) downwards in MNI space | -b |
debug |
boolean |
No | Debug mode (keep intermediate files) | -d |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - lesion_mask:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
output_directory |
Directory |
$(inputs.output_dir || inputs.input.nameroot + '_sienax') |
report |
File |
$(inputs.output_dir || inputs.input.nameroot + '_sienax')/report.sienax |
brain_volume |
File |
$(inputs.output_dir || inputs.input.nameroot + '_sienax')/*_brain.nii.gz, $(inputs.output_dir || inputs.input.nameroot + '_sienax')/*_brain.nii |
segmentation |
File |
$(inputs.output_dir || inputs.input.nameroot + '_sienax')/*_seg.nii.gz, $(inputs.output_dir || inputs.input.nameroot + '_sienax')/*_seg.nii |
log |
File |
sienax.log |
Output Extensions¶
- report:
.sienax - brain_volume:
.nii,.nii.gz - segmentation:
.nii,.nii.gz
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¶
- Structural MRI > FSL > Pipelines
- Pipelines > FSL > Structural