fsl-tool

FSL Tool

Overview

FSL is a comprehensive library of analysis tools for MRI, fMRI, and diffusion brain imaging. This skill provides a safe, unified interface for the three core modalities in NeuroClaw:

• Structural MRI (T1w, T2w, FLAIR)
• Functional MRI (task-based and resting-state)
• Diffusion MRI (DTI / dMRI)

Workflow:

1. Check if FSL is installed (fslversion).
2. If not installed → call dependency-planner to generate installation plan.
3. Analyze input files and propose concrete shell commands with parameter explanations.
4. Present full numbered plan + estimated time + risks.
5. Wait for explicit user confirmation (“YES”, “execute”, “proceed”).
6. Execute all commands safely via claw-shell.
7. Summarize outputs and suggest next steps.

Research use only.

Core Modalities and Common Shell Commands

1. Structural MRI

# One-click structural preprocessing (strongly recommended)
fsl_anat -i T1w.nii.gz -o T1w_anat --clobber
# -i : input T1w file
# -o : output folder name
# --clobber : overwrite existing files (commonly used)

# Brain extraction (BET)
bet T1w.nii.gz T1w_brain -m -f 0.5
# -m : output brain mask (_mask.nii.gz)
# -f : brain extraction threshold (0.3~0.7; 0.5 is usually stable)

# Tissue segmentation + bias correction
fast -t 1 -n 3 -H 0.1 -I 4 -l 20.0 -o T1w_fast T1w_brain
# -t 1 : T1-weighted image
# -n 3 : 3 tissue classes (GM, WM, CSF)
# -H 0.1 : bias field correction strength

# Linear + nonlinear registration to MNI152
flirt -in T1w_brain -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain -out T1w_to_MNI -omat T1w_to_MNI.mat -dof 12
fnirt --in=T1w_brain --aff=T1w_to_MNI.mat --cout=T1w_to_MNI_warp --config=T1_2_MNI152_2mm

# Subcortical segmentation
first -i T1w_brain -o T1w_first -b

2. Functional MRI

# Motion correction
mcflirt -in bold.nii.gz -out bold_mcf -plots -refvol 0

# Task-based fMRI full analysis (FEAT)
feat design.fsf

# Resting-state ICA
melodic -i bold_mcf.nii.gz -o melodic_output --report --nobet --bgthreshold=10 --tr=2.0 --mmthresh=0.5 --dim=30

# Automatic denoising (FIX)
fix melodic_output -c $FSLDIR/training_files/Standard.RData -m -f 20