FMRIB's Integrated Registration and Segmentation Tool (FIRST)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Multi-step pipeline for subcortical structure segmentation. Internally chains registration, boundary correction, and shape-model segmentation for 15 subcortical structures.
Modality: T1-weighted 3D NIfTI volume (does not need to be brain-extracted).
Typical Use: Volumetric analysis of subcortical structures (hippocampus, amygdala, caudate, etc.).
Key Parameters¶
-i (input image), -o (output basename), -b (run BET first), -s (comma-separated structures list)
Key Points¶
Models 15 subcortical structures. Outputs meshes (.vtk) and volumetric labels. Can run on selected structures only with -s flag.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input T1-weighted image | -i |
output |
string |
Yes | Output basename | -o |
brain_extracted |
boolean |
No | Input is already brain extracted | -b |
method |
enum |
No | Boundary correction method | -m |
structures |
string |
No | Run only on specified structures (comma-separated list) | -s |
affine |
File |
No | Use this affine matrix for registration | -a |
three_stage |
boolean |
No | Use 3-stage registration | -3 |
verbose |
boolean |
No | Verbose output | -v |
debug |
boolean |
No | Debug mode (don't delete temporary files) | -d |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - affine:
.mat
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
segmentation_files |
File[] |
$(inputs.output)_all_fast_firstseg.nii.gz, $(inputs.output)_all_fast_origsegs.nii.gz, $(inputs.output)-*_first.nii.gz |
vtk_meshes |
File[] |
$(inputs.output)-*.vtk |
bvars |
File[] |
$(inputs.output)-*.bvars |
log |
File |
run_first_all.log |
Output Extensions¶
- segmentation_files:
.nii.gz - vtk_meshes:
.vtk - bvars:
.bvars
Enum Options¶
method: auto, fast, none
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 > Tissue Segmentation
- Pipelines > FSL > Structural