Structural Image Evaluation using Normalisation of Atrophy (SIENA)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Multi-step pipeline that estimates percentage brain volume change between two timepoints. Internally chains BET brain extraction, registration, FAST segmentation, and edge-point displacement analysis.
Modality: Two T1-weighted 3D NIfTI volumes from different timepoints.
Typical Use: Measuring brain volume change over time (e.g., atrophy in neurodegeneration).
Key Parameters¶
-o (output directory), -BET (BET options), -2 (2-class segmentation), -S (SIENA step options)
Key Points¶
Requires two scans of same subject at different timepoints. Reports percentage brain volume change (PBVC). Accurate to ~0.2% volume change.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input1 |
File |
Yes | Input T1 image (timepoint 1) | |
input2 |
File |
Yes | Input T1 image (timepoint 2) | |
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 | Inputs are T2-weighted | -t2 |
std_masking |
boolean |
No | Apply standard-space masking for difficult cases | -m |
siena_diff_options |
string |
No | Options to pass to siena_diff (e.g., "-s -i 20") | -S |
ventricle_analysis |
boolean |
No | Activate ventricular analysis (VIENA) | -V |
ventricle_mask |
File |
No | Custom ventricle mask | -v |
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¶
- input1:
.nii,.nii.gz - input2:
.nii,.nii.gz - ventricle_mask:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
output_directory |
Directory |
$(inputs.output_dir || '*_to_*_siena') |
report |
File |
$(inputs.output_dir || '*_to_*_siena')/report.siena |
pbvc |
File |
$(inputs.output_dir || '*_to_*_siena')/report.sienax |
edge_points |
File[] |
$(inputs.output_dir || '*_to_*_siena')/*_edge*.nii.gz, $(inputs.output_dir || '*_to_*_siena')/*_edge*.nii |
flow_images |
File[] |
$(inputs.output_dir || '*_to_*_siena')/*_flow*.nii.gz, $(inputs.output_dir || '*_to_*_siena')/*_flow*.nii |
log |
File |
siena.log |
Output Extensions¶
- report:
.siena - pbvc:
.sienax - edge_points:
.nii,.nii.gz - flow_images:
.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