Imaging Study Design and Biomarker Selection

Overview

This skill encodes methodology for designing medical imaging studies and selecting imaging biomarkers. It guides decisions about preprocessing, registration targets, de-identification, biomarker choice, radiomics stability, and multi-site harmonization. It is a reasoning skill — it does not generate pipeline code. For concrete tooling (FreeSurfer, FSL, ANTs, PyRadiomics, nnU-Net, MONAI), pair this skill with a pipeline skill after the study design is settled.

The central principle: preprocessing and biomarker choice must preserve the signal that answers the clinical question. A pipeline that is standard for one question (e.g., MNI registration for group comparison) can destroy the signal for another (e.g., individual atrophy in longitudinal studies).

Usage

Invoke this skill when planning an imaging study or critiquing an existing imaging pipeline. Typical prompts:

• "I want to measure hippocampal atrophy over 2 years in Alzheimer's patients — how should I preprocess?"
• "Design a multi-site radiomics study for NSCLC prognosis."
• "We're collecting brain MRI across three scanners. What harmonization do I need?"
• "Is it safe to share these DICOMs after standard de-identification?"
• "Which imaging biomarker should I use for presurgical mapping in epilepsy?"

Use the Decision Framework at the end of Core Concepts to structure any imaging study question.