Agent skill · Data & Analytics

fsl-tool

Use this skill whenever the user wants to process neuroimaging data with FSL (FMRIB Software Library), covering structural MRI, functional MRI (fMRI), and diffusion MRI (dMRI/DTI). Triggers include: 'use FSL', 'FSL processing', 'fsl_anat', 'FEAT', 'MELODIC', 'eddy', 'bedpostx', 'probtrackx', 'BET', 'FAST', 'FLIRT', 'FNIRT', 'run FSL pipeline'. This skill is the NeuroClaw interface-layer wrapper for FSL: checks installation, generates execution plan with concrete shell commands, waits for explicit confirmation, then routes all commands through claw-shell.

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill fsl-tool --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 1
SKILL.md size: 8 KB
Bundled scripts: none
Requires: - claw-shell
Path: skills/neuroclaw/fsl-tool/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the SKILL.md

# 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 ```bash # 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 thresh

What's inside
Steps it walks through
  1. Overview
  2. Core Modalities and Common Shell Commands
  3. 1. Structural MRI
  4. 2. Functional MRI
  5. 3. Diffusion MRI
  6. Quick Reference
  7. Installation
  8. Important Notes & Limitations
  9. When to Call This Skill
  10. Complementary / Related Skills
  11. More Advanced Features
  12. Post-Execution Verification (Harness Integration)
Commands it runs
One-click structural preprocessing (strongly recommended)
fsl_anat -i T1w.nii.gz -o T1w_anat --clobber
Brain extraction (BET)
bet T1w.nii.gz T1w_brain -m -f 0.5
Tissue segmentation + bias correction
fast -t 1 -n 3 -H 0.1 -I 4 -l 20.0 -o T1w_fast T1w_brain
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
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About this skill
What does the fsl-tool skill do?

Use this skill whenever the user wants to process neuroimaging data with FSL (FMRIB Software Library), covering structural MRI, functional MRI (fMRI), and diffusion MRI (dMRI/DTI). Triggers include: 'use FSL', 'FSL processing', 'fsl_anat', 'FEAT', 'MELODIC', 'eddy', 'bedpostx', 'probtrackx', 'BET', 'FAST', 'FLIRT', 'FNIRT', 'run FSL pipeline'. This skill is the NeuroClaw interface-layer wrapper for FSL: checks installation, generates execution plan with concrete shell commands, waits for explicit confirmation, then routes all commands through claw-shell.

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill fsl-tool --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.

Where does this skill come from?

From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.

Is a popular skill a good skill?

Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.

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