CentileBrain - Generate Normative Deviation Values

URL: https://centilebrain.org/#/model

Generates z-scores for a single subject's FreeSurfer-derived morphometry against the CentileBrain normative reference. Three separate modalities (SubcorticalVolume, CorticalThickness, SurfaceArea), two sexes, each a distinct Shiny app. Login/account not required.

Site shape

• The /#/model page is a thin wrapper around per-modality/sex Shiny iframes at https://centilebrain-app.shinyapps.io/{SV|CT|SA}-{MALE|FEMALE}/.
• Switching modality swaps the iframe; switching sex swaps the iframe. The top-page buttons and toggles are not forms - they just replace the iframe src.
• The upload form, compute button, and download link all live inside the iframe. iframe_target("shinyapps.io/SV-MALE") (etc.) returns the session to use.
• Requires upload_file(..., target_id=...) - the iframe-aware upload helper.

Form elements (inside the iframe)

Waits

• Upload: after upload_file, wait ~3 s for the Shiny server to read the file; the data preview table populates in-place.
• 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.
• 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.

Traps

• 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.
• 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()").
• 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.

End-to-end example

import time, os
 
DL = "/tmp/centilebrain"
os.makedirs(DL, exist_ok=True)
cdp("Browser.setDownloadBehavior", behavior="allow", downloadPath=DL, eventsEnabled=True)
 
new_tab("https://centilebrain.org/#/model")
wait_for_load()
time.sleep(2)
 
# Pick modality + sex (SV + male shown; repeat for CT and SA as needed)
js("""Array.from(document.querySelectorAll('button'))
       .find(b => b.innerText.trim() === 'SUBCORTICAL VOLUME').click()""")
time.sleep(1)
js("document.querySelector('input[name=male]').click()")
time.sleep(2)
 
t = iframe_target("shinyapps.io/SV-MALE")
upload_file("#file1", "/abs/path/JMT_subcortical_volume.xlsx", target_id=t)
time.sleep(3)
 
js("""const e=document.querySelector('#email');
      e.value='user@example.com';
      e.dispatchEvent(new Event('input',{bubbles:true}));""", target_id=t)
 
js("document.querySelector('#confirm').click()", target_id=t)
for _ in range(40):
    time.sleep(3)
    if "Computation complete" in js("document.body.innerText", target_id=t):
        break
 
before = set(os.listdir(DL))
js("document.querySelector('#downloadData1').click()", target_id=t)
for _ in range(30):
    time.sleep(2)
    after = set(os.listdir(DL))
    new = after - before
    if new and not any(f.endswith(".crdownload") for f in after):
        print("downloaded:", new)
        break

Output zip

Unzipped contents (SV example):

output_file_YYYY-MM-DD-HH-MM-SS/
  zscore_SubcorticalVolume_male.csv       # per-ROI z-scores
  prediction_SubcorticalVolume_male.csv   # model-predicted raw values
  centile_SubcorticalVolume_male.xlsx     # centile ranks
  MAE_SubcorticalVolume_male.csv          # model accuracy (not per-subject)
  RMSE_SubcorticalVolume_male.csv
  Corr_SubcorticalVolume_male.csv
  EV_SubcorticalVolume_male.csv

The zscore_*.csv is the file you almost always want. Columns are SITE, SubjectID, Vendor, FreeSurfer_Version, age, <ROIs...>.

Multi-subject / batch uploads

The .xlsx template accepts many rows, and CentileBrain processes them all in one compute. Same flow, same iframe; the z-score CSV will have one row per subject. No concurrency needed across modality/sex for a typical cohort.

generate-estimates.md · updated Apr 28, 2026 · 594 words