110 lines
5.1 KiB
Markdown
110 lines
5.1 KiB
Markdown
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# CentileBrain — Generate Normative Deviation Values
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URL: `https://centilebrain.org/#/model`
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Generates z-scores for a single subject's FreeSurfer-derived morphometry
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against the CentileBrain normative reference. Three separate modalities
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(`SubcorticalVolume`, `CorticalThickness`, `SurfaceArea`), two sexes,
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each a distinct Shiny app. Login/account not required.
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## Site shape
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- The `/#/model` page is a thin wrapper around per-modality/sex **Shiny
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iframes** at `https://centilebrain-app.shinyapps.io/{SV|CT|SA}-{MALE|FEMALE}/`.
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- Switching modality swaps the iframe; switching sex swaps the iframe.
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The top-page buttons and toggles are not forms — they just replace
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the iframe `src`.
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- The upload form, compute button, and download link all live **inside the iframe**.
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`iframe_target("shinyapps.io/SV-MALE")` (etc.) returns the session to use.
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- Requires `upload_file(..., target_id=...)` — the iframe-aware upload helper.
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## Form elements (inside the iframe)
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| Selector | Purpose |
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|---|---|
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| `#email` | Required text input. Any valid-looking string works; it does not send mail. |
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| `#file1` | The file input. Accepts the official `.xlsx` template for that modality/sex (download from the site to see the expected schema). |
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| `#confirm` | The **Compute** button. Click exactly once after upload. |
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| `#downloadData1` | **Download Results** link once compute is done. Produces a zip of CSVs + xlsx. |
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## Waits
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- Upload: after `upload_file`, wait ~3 s for the Shiny server to read the file; the data preview table populates in-place.
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- Compute: poll the iframe body text for `"Computation complete"` — typically 30-90 s. `"Computing… This may take a few seconds to a couple of minutes."` is the in-progress marker.
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- Download: click `#downloadData1`, then poll the Chrome download directory for a `{SV|CT|SA}_{male|female}_YYYY-MM-DD-HH-MM-SS.zip`. Set `Browser.setDownloadBehavior` with a known `downloadPath` before clicking so you can find it deterministically.
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## Traps
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- **Iframe target_id goes stale across modality swaps.** After clicking `CORTICAL THICKNESS` or `SURFACE AREA`, re-call `iframe_target("shinyapps.io/CT-MALE")` — the old id from SV-MALE will not work even though `Target.getTargets` may still list it briefly. Add a 2-3 s sleep after the modality-swap click before re-resolving.
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- **Sex toggles are MUI switches, not radio buttons.** They are `input[type=checkbox]` with `name=female` / `name=male`. Clicking one does not automatically uncheck the other visibly, but the iframe src changes based on which is `checked`. Easiest: `js("document.querySelector('input[name=male]').click()")`.
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- **Top-level buttons scroll off-screen after first interaction.** The modality buttons are at `y ≈ 226`, but after scrolling/iframe expansion they report `y < 0`. Use `js("window.scrollTo(0, 0)")` then click via JS by text (`Array.from(document.querySelectorAll('button')).find(b => b.innerText.trim() === 'CORTICAL THICKNESS').click()`) instead of fixed coordinates.
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## End-to-end example
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```python
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import time, os
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DL = "/tmp/centilebrain"
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os.makedirs(DL, exist_ok=True)
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cdp("Browser.setDownloadBehavior", behavior="allow", downloadPath=DL, eventsEnabled=True)
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new_tab("https://centilebrain.org/#/model")
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wait_for_load()
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time.sleep(2)
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# Pick modality + sex (SV + male shown; repeat for CT and SA as needed)
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js("""Array.from(document.querySelectorAll('button'))
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.find(b => b.innerText.trim() === 'SUBCORTICAL VOLUME').click()""")
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time.sleep(1)
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js("document.querySelector('input[name=male]').click()")
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time.sleep(2)
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t = iframe_target("shinyapps.io/SV-MALE")
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upload_file("#file1", "/abs/path/JMT_subcortical_volume.xlsx", target_id=t)
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time.sleep(3)
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js("""const e=document.querySelector('#email');
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e.value='[email protected]';
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e.dispatchEvent(new Event('input',{bubbles:true}));""", target_id=t)
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js("document.querySelector('#confirm').click()", target_id=t)
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for _ in range(40):
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time.sleep(3)
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if "Computation complete" in js("document.body.innerText", target_id=t):
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break
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before = set(os.listdir(DL))
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js("document.querySelector('#downloadData1').click()", target_id=t)
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for _ in range(30):
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time.sleep(2)
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after = set(os.listdir(DL))
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new = after - before
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if new and not any(f.endswith(".crdownload") for f in after):
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print("downloaded:", new)
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break
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```
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## Output zip
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Unzipped contents (SV example):
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```
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output_file_YYYY-MM-DD-HH-MM-SS/
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zscore_SubcorticalVolume_male.csv # per-ROI z-scores
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prediction_SubcorticalVolume_male.csv # model-predicted raw values
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centile_SubcorticalVolume_male.xlsx # centile ranks
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MAE_SubcorticalVolume_male.csv # model accuracy (not per-subject)
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RMSE_SubcorticalVolume_male.csv
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Corr_SubcorticalVolume_male.csv
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EV_SubcorticalVolume_male.csv
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```
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The `zscore_*.csv` is the file you almost always want. Columns are
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`SITE, SubjectID, Vendor, FreeSurfer_Version, age, <ROIs...>`.
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## Multi-subject / batch uploads
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The `.xlsx` template accepts many rows, and CentileBrain processes them
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all in one compute. Same flow, same iframe; the z-score CSV will have
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one row per subject. No concurrency needed across modality/sex for a
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typical cohort.
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