preprocess-debug
Debug preprocessing pipeline failures. Guides through reading checkpoint files, checking step artifacts, interpreting QC metrics, examining visualization PNGs, and identifying which step failed and why. Use when a preprocessing run produces unexpected results, crashes, or generates poor-quality outputs.
npx skills add majiayu000/claude-skill-registry --skill preprocess-debug --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Preprocess Debug — Preprocessing Failure Diagnosis ## When to Use - "Why did preprocessing fail for patient X?" - "The registration output looks wrong" - "Skull stripping removed too much / too little" - "Intensity normalization produced weird values" - "Which step is causing the problem?" - Any preprocessing quality issue or crash investigation ## Diagnostic Workflow ### Step 1: Identify the failing step Check the visualization directory for which step produced the last PNG: ```bash ls -la {viz_root}/MenGrowth-XXXX/MenGrowth-XXXX-YYY/ # step1_data_harmonization_t1c.png ← exists # step2_bias_field_correction_t1c.png ← exists # step3_resampling_t1c.png ← MISSING → Step 3 failed ``` Check logs for error messages (look for `ERROR` or `RuntimeError`). ### Step 2: Check step artifacts Each step may produce artifacts in `{artifacts}/MenGrowth-XXXX/MenGrowth-XXXX-YYY/`: | Artifact | Produced by | What to check | |----------|-------------|---------------| | `t1c_bias_field.nii.gz` | Bias field correction | Should be smooth, low-frequency field | | `t1c_brain_mask.nii.gz` | Skull stripping | Load in viewer — verify mask covers brain + tumor | | `*.h5`, `*.mat` transforms | Registration |
- When to Use
- Diagnostic Workflow
- Step 1: Identify the failing step
- Step 2: Check step artifacts
- Step 3: Examine visualization PNGs
- Step 4: Check specific failure patterns
- Step 5: Check the temp-file mechanism
- Key Debugging Code Locations
- Quick Config Fixes
ls -la {viz_root}/MenGrowth-XXXX/MenGrowth-XXXX-YYY/
step1_data_harmonization_t1c.png ← exists
step2_bias_field_correction_t1c.png ← exists
step3_resampling_t1c.png ← MISSING → Step 3 failed
find {output_root} -name "*.tmp*"What does the preprocess-debug skill do?
Debug preprocessing pipeline failures. Guides through reading checkpoint files, checking step artifacts, interpreting QC metrics, examining visualization PNGs, and identifying which step failed and why. Use when a preprocessing run produces unexpected results, crashes, or generates poor-quality outputs.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill preprocess-debug --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 majiayu000/claude-skill-registry, a repository with 534 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.