Plan FreeSurfer recon-all cortical workflows and route surface outputs.
npx skills add https://github.com/MarvinCui/NeuroForge --skill freesurfer
Please help me install this Agent Skill. Skill: freesurfer Source: https://github.com/MarvinCui/NeuroForge/tree/main/NeuroForge/skills/freesurfer Command: npx skills add https://github.com/MarvinCui/NeuroForge --skill freesurfer
It helps you understand, route, and plan FreeSurfer cortical surface reconstruction and anatomical processing tasks without guessing command details or making unsafe assumptions.
Use the freesurfer skill for a question about what recon-all steps produce which cortical surface outputs and what QC checks to run before continuing.
High-intent search queries and answers about installing and using this skill.
Recon-all generates cortical surface outputs through sequential anatomical segmentation and surface reconstruction stages, with expected outputs mapped in local recon-all step tables for reference.
Plan FreeSurfer QC inspection by checking cortical surfaces, parcellations, and coordinate assumptions, routing outputs to downstream tool families like MNE or Nilearn for safe next steps.
FreeSurfer coordinate systems support routing to MNE or Nilearn pipelines, with documentation covering coordinate assumptions and file formats to ensure safe downstream multimodal analysis.
FreeSurfer segmentation artifacts to watch for include surface reconstruction errors and parcellation defects, identifiable through planned QC inspection steps before continuing heavy processing.
Avoid running heavy FreeSurfer processing when planning or routing tasks are needed instead, as this support focuses on documentation, high-level output interpretation, and safe workflow inspection.
NeuroAIHubExecute containerized BIDS-App fMRI preprocessing with motion correction and anatomical registration.
CUHK-AIM-GroupTranslate neuroimaging outputs into publication-ready figures and 3D meshes.
NeuroAIHubGenerate 2D flatmaps and 3D WebGL viewers from fMRI data using pycortex.
AlexiosBluffMaraAnalyze cortical responses from media stimuli using Cortex's TRIBE v2 pipeline.
