| --- |
| title: PPMI Mini |
| tags: |
| - medical-imaging |
| - mri |
| - nifti |
| - parkinsons |
| - ppmi |
| --- |
| |
| # PPMI Mini |
|
|
| A 1,000-subject PPMI sMRI evaluation subset derived from local BIDS T1w images |
| and PPMI subject-characteristics metadata. |
|
|
| ## Cohort |
|
|
| - 1,000 subjects / 1,000 scans |
| - One T1w scan per subject |
| - Sex: 431 Female / 569 Male |
| - Diagnosis: CN 226 / PD 357 / Prodromal 356 / SWEDD 61 |
|
|
| ## Features |
|
|
| The dataset has a single `eval` split with embedded NIfTI image bytes in `nifti`. |
| Brain masks and SynthSeg volumes are intentionally omitted for v0.1. |
|
|
| ## Clinical targets |
|
|
| `clinical/ppmi_mini_clinical.parquet` holds derived clinical targets for the same |
| 1,000 scans, joined from PPMI LONI study data. It is a sidecar table rather than |
| extra columns on the split, so the imaging is untouched. |
|
|
| ```python |
| from datasets import load_from_disk |
| from huggingface_hub import snapshot_download, hf_hub_download |
| import pandas as pd |
| |
| data = load_from_disk(snapshot_download("medarc/ppmi-mini", repo_type="dataset"))["eval"] |
| clinical = pd.read_parquet( |
| hf_hub_download("medarc/ppmi-mini", "clinical/ppmi_mini_clinical.parquet", repo_type="dataset") |
| ).set_index("sample_id") |
| clinical = clinical.loc[list(data["sample_id"])] # aligned to the split |
| ``` |
|
|
| ### Keys |
|
|
| | Column | Meaning | |
| |:---|:---| |
| | `sample_id` | Joins to the split. One row per scan. | |
| | `participant_id` | Subject, `sub-<PATNO>`. Use it to group by subject in cross-validation. | |
|
|
| The raw PPMI `PATNO` is not included; `participant_id` already encodes it. |
|
|
| ### Longitudinal targets |
|
|
| Each instrument below yields three columns: `<prefix>_baseline`, the score |
| measured nearest the scan; `<prefix>_slope_48m`, the annualized OLS slope over |
| visits in a −0.25 to 4.0 year window relative to the scan, requiring at least 2 |
| visits at distinct dates; and `<prefix>_n_visits`, how many visits fed the fit. |
| A slope is null where the participant has too few visits in the window. |
|
|
| | Prefix | Instrument | Range | Direction | n (baseline / slope) | |
| |:---|:---|:---|:---|:---| |
| | `np3tot_off` | MDS-UPDRS Part III motor exam, OFF-medication and untreated exams only | 0–132 | higher = worse | 810 / 765 | |
| | `np3tot_all` | MDS-UPDRS Part III, all medication states | 0–132 | higher = worse | 992 / 953 | |
| | `nhy_off` | Hoehn & Yahr stage, OFF-medication and untreated | 0–5 ordinal | higher = worse | 809 / 763 | |
| | `nhy_all` | Hoehn & Yahr stage, all medication states | 0–5 ordinal | higher = worse | 991 / 951 | |
| | `np2ptot` | MDS-UPDRS Part II, patient-reported motor experiences of daily living | 0–52 | higher = worse | 998 / 971 | |
| | `mseadlg` | Modified Schwab & England ADL, percent independence | 0–100 | higher = better | 849 / 812 | |
| | `mcatot` | Montreal Cognitive Assessment | 0–30 | higher = better | 992 / 921 | |
| | `cogcomp` | Cognitive composite, see below | SD units | higher = better | 987 / 930 | |
| | `sbr_striatum` | DAT-SPECT striatal binding ratio, whole striatum, referenced to occipital white matter | continuous | lower = more dopaminergic loss | 712 / 440 | |
| | `sbr_putamen` | Same, putamen, where loss appears earliest in PD | continuous | lower = more loss | 712 / 440 | |
| | `sbr_caudate` | Same, caudate | continuous | lower = more loss | 712 / 440 | |
|
|
| MDS-UPDRS Part III is scored either ON or OFF dopaminergic medication, and ON |
| scores are drug-suppressed, so the `_off` and `_all` variants are both provided: |
| `_off` is the cleaner target, `_all` has the larger sample. |
|
|
| `cogcomp` is the mean z-score across five full-length neuropsychological tests — |
| HVLT-R total recall, Symbol Digit Modalities, Benton Judgement of Line |
| Orientation, Letter–Number Sequencing and semantic (animal) fluency — requiring |
| at least 3 of the 5 present at a visit. Each test is z-scored across all study |
| visits before averaging. Raw totals are used rather than PPMI's derived |
| age-normed T-scores, so that age is not silently removed from the target. |
|
|
| It is provided because MoCA ceilings in this cohort: 66.7% of participants score |
| ≥27/30 and 12.2% sit at exactly 30, so MoCA cannot resolve variation in the |
| normal range. |
|
|
| ### Cross-sectional targets |
|
|
| | Column | Meaning | Range | Direction | n | |
| |:---|:---|:---|:---|:---| |
| | `upsit_baseline` | University of Pennsylvania Smell Identification Test, 40 items | 0–40 | higher = better | 386 | |
| | `rbdsq_baseline` | REM Sleep Behaviour Disorder Screening Questionnaire | 0–13 | higher = more symptoms | 990 | |
| | `saa_positive` | CSF alpha-synuclein seed amplification assay | 1 = positive | — | 910 | |
| | `prs_meta5` | PD polygenic risk score, META5 | continuous | higher = more risk | 827 | |
| | `prs_meta5_excl_lrrk2_gba` | Same score with the *LRRK2* and *GBA* loci removed | continuous | higher = more risk | 827 | |
|
|
| `saa_positive` has no specimen collection date in the source, only a visit code |
| and an assay run date, so unlike every other column it is not time-aligned to |
| the scan. One status per subject is taken, preferring the baseline visit. |
| Inconclusive results are dropped rather than coerced. Positivity by group is |
| CN 5.6%, Prodromal 51.3%, PD 90.3%, so it is close to a diagnosis label. |
|
|
| PPMI ships the RBDSQ as individual items rather than a total, so |
| `rbdsq_baseline` sums items 1–12 and adds 1 for item 13 if any neurological |
| condition is present; note that `PTCGBOTH` in that source file is not a score |
| but a record of whether the participant, the caregiver or both completed the |
| form. And `NHY` values of `101` in the source are an out-of-range "not assessed" |
| sentinel, mapped to null here. |
|
|
| ### Recruitment covariates |
|
|
| | Column | Meaning | |
| |:---|:---| |
| | `enrolled_genetic_cohort` | 1 if enrolled via *LRRK2*, *GBA*, *SNCA*, *PINK1* or *PRKN* carrier status (149 of 1000) | |
| | `enrolled_hyposmia` | 1 if enrolled via the hyposmia pathway (197) | |
| | `enrolled_rbd` | 1 if enrolled via the RBD pathway (77) | |
|
|
| These are covariates, not targets. PPMI recruits genetic carriers through a |
| dedicated cohort, and that membership correlates with PD polygenic risk at |
| r = 0.58 by construction, so any target that might vary with recruitment should |
| be checked against these. The two PRS variants are shipped together for the same |
| reason, to separate cohort enrichment from the rest of the polygenic signal. |
|
|
