Package index • ADNIMERGE2

ADNI Raw Datasets

All Alzheimer’s Disease Neuroimaging Initiative (ADNI) study data as shared at https://adni.loni.usc.edu/.

Data Dictionary - DATADIC

DATADIC: Data Dictionary Dataset - Updated

REMOTE_DATADIC: Remote Collected Data Dictionary Dataset

Subject Characteristics

Includes subject demographics, and family history

ADI: Area Deprivation Index Score

AMAS: Abbreviated Multidimensional Acculturation Scale

FAMHXPAR: Family History - Parents

FAMHXSIB: Family History - Sibling Log

FHQ: Family History Questionnaire

PTDEMOG: Participant Demographic Information

RECFHQ: Family History Questionnaire Subtable

RURALITY: Rurality – RUCA & RUCC

Enrollment

Includes amyloid status and amyloid disclosure results, and enrollment-related dataset

ADDCOMM: Additional Comments

ADNI2_VISITID: ADNI2 Visit Code Mapping List

AMYDISC: Amyloid Disclosure Visit

AMYREAD: Amyloid PET Read

ARM: ARM

CLIELG: Clinician Verification

CONSENTS: Consent Tracking

EBISU: Ebisu (ADNI ONLINE) ID

EXCLUSIO: Exclusion Criteria

INCLUSIO: Inclusion Criteria

NPSTATUS: Neuropathology Status

POSAMYDISC: Post-Amyloid PET Disclosure

PREAMYDISC: Pre-Amyloid PET Disclosure

PUBLICITY: Recruitment Tracking

REGISTRY: Registry

ROSTER: Roster

STUDYSUM: Study Visits Summary

TREATDIS: Early Discontinuation and Withdrawal

VISITS: VISITS

Medical History

Includes adverse events, concurrent medications (drugs), medical history/ initial health assessments, and phyiscal/neurological exams

ADNI2_ECG: ECG

ADVERSE: Adverse Events Log

ANTIAMYTX: Anti-Amyloid Treatment Information

AV45FOLLOW: AV-45 24-48 Hour Follow-Up

AV45VITALS: AV-45 Pre and Post Injection Vitals

BACKMEDS: Key Background Medications

BLSCHECK: Baseline Symptoms Checklist

INITHEALTH: Initial Health Assessment

MEDHIST: Medical History

NEUROEXM: Neurological Exam

PHYSICAL: Physical Exam

RECADV: Adverse Events/Hospitalizations - Log

RECBLLOG: Documentation of Baseline Symptoms Log

RECCMEDS: Concurrent Medications Log

RECMHIST: Medical History

VITALS: Vital Signs

Assessments

Includes clinical diagnostics summary, neuropsychological assessment results, and non-clinical assessments such as result from the Brain Health Registry (BHR)

ADAS: ADAS-Cognitive Behavior

ADSXLIST: Diagnosis and Symptoms Checklist

AMNART: American National Adult Reading Test

BHR: Brain Health Registry (BHR)

BHR_BASELINE_QUESTIONNAIRE: Brain Health Registry (BHR) BASELINE QUESTIONNAIRE

BHR_EVERYDAY_COGNITION: Brain Health Registry (BHR) EVERYDAY COGNITION

BHR_LONGITUDINAL_QUESTIONNAIRE: Brain Health Registry (BHR) LONGITUDINAL QUESTIONNAIRE

BHR_MEMTRAX: Brain Health Registry (BHR) MEMTRAX

BHR_SP_ADL: Brain Health Registry (BHR) SP ADL

BHR_SP_CAREGIVER_BURDEN: Brain Health Registry (BHR) SP CAREGIVER BURDEN

BHR_SP_EVERYDAY_COGNITION: Brain Health Registry (BHR) SP EVERYDAY COGNITION

BHR_SP_FAQ: Brain Health Registry (BHR) SP FAQ

BHR_SP_INITIAL: Brain Health Registry (BHR) SP INITIAL

BHR_SP_RELATIONSHIP: Brain Health Registry (BHR) SP RELATIONSHIP

BHR_SP_STUDY_CONFIRMATION: Brain Health Registry (BHR) SP STUDY CONFIRMATION

BLCHANGE: Diagnostic Summary - Baseline Changes

CBBCOMP: Cogstate Brief Battery

CBBRESULTS: Cogstate Battery Results

CCI: Cognitive Change Index

CDR: Clinical Dementia Rating

CSSRSAD: Columbia- Suicide Severity Rating Scale (C-SSRS) + AD Specific Suicide

DXSUM: Diagnostic Summary

ECOG12PT: Everyday Cognition 12 Item - Participant Self-Report

ECOG12SP: Everyday Cognition 12 Item - Study Partner Report

ECOGPT: Everyday Cognition - Participant Self-Report

ECOGSP: Everyday Cognition - Study Partner Report

EMBICDCB: Embic Corporation – Digital Cognitive Biomarkers

EMBICqCP: Embic Corporation Quantified Cognitive Processes

FAQ: Functional Assessment Questionnaire

FCI: Financial Capacity Instrument Short Form (FCI-SF)

GDSCALE: Geriatric Depression Scale

IES: Impact of Events Scale

ITEM: Item Level Data

MMSE: Mini Mental State Exam

MOCA: MoCA

MODHACH: Modified Hachinski

NEUROBAT: Neuropsychological Battery

NPI: Neuropsychiatric Inventory

NPIQ: Neuropsychiatric Inventory Q

PEDQCV: Brief Perceived Ethnic Discrimination Questionnaire-Community Version

PSS: Perceived Stress Scale 10 Item

RYFF: RYFF Psychological Well-Being Purpose in Life

STAIAD: Mini-State Trait Anxiety Inventory (STAI) for Adults™

UWNPSYCHSUM: Crane Lab (UW) Neuropsych Summary Scores

WATC: Word Accentuation Test - Chicago

Imaging

Includes image acquisition, image analysis results, image quality for both MIR and PET

ADNI2_OTELGTAU: Tau AV-1451 PET Eligibility

AMYMETA: Amyloid PET Scan Information

AMYQC: Amyloid PET QC

AV45META: AV-45 PET Scan Information

AV45QC: AV-45 PET QC Tracking

BAIMRINMRC: BAI - MRI NMRC Summaries: 2016-09-12

BAINMRC: BAI - NMRC Summaries

BAIPETNMRC: BAI - PET NMRC Summaries: 2018-04-12

BAIPETNMRCAV45: BAI - PET NMRC AV45 Summaries: 2020-10-23

BAIPETNMRCFDG: BAI - PET NMRC FDG Summaries: 2020-12-11

BAIPETNMRCFTP: BAI - PET NMRC Flortaucipir (F-AV1451) Summaries: 2022-08-17

BSI: Boundary Shift Integral Summaries (Nick Fox's lab)

CROSSVAL: CROSSVAL

Changed_Study_ID_Listing: CHANGED_STUDY_ID_LISTING

DTIROI_MEAN: USC - DTI ROI Summary Measures v2 + v3 (Mean)

DTIROI_ROBUSTMEAN: USC - DTI ROI Summary Measures v2 + v3 (Robust Mean)

DTIROI_V1: USC - DTI ROI Summary Measures v1

FOXLABBSI: Fox Lab BSI measures

MAYOADIRL_MRI_FMRI: Jack Lab - Default Mode Network connectivity: 2017-11-07

MAYOADIRL_MRI_FMRI_NFQ: Jack Lab - fMRI Network Failure Quotient (NFQ)

MAYOADIRL_MRI_MCH: Jack Lab - ADNI MRI MCH

MAYOADIRL_MRI_QUALITY_ADNI3: MAYOADIRL_MRI_QUALITY_ADNI3

MAYOADIRL_MRI_TBMSYN: Jack Lab - TBM-SyN Based Scores

MRI3META: 3T MRI Scan Information

MRIB1CALIB: MRI B1 Calibration

MRIFind: MAYO ADIR LAB MRI Findings

MRIMETA: 1.5T MRI Scan Information

MRIMPPRO: MRI MPRAGE Process

MRIMPRANK: MRI MPRAGE Ranking

MRINCLUSIO: MRI Subject Inclusion

MRINFQ: MAYO ADIR LAB MRI Network Failure Quotient

MRIPROT: MRI Protocol

MRIQC: MAYO ADIR LAB MRI Quality

MRIQSM: MAYO ADIR LAB MRI Quantitative Susceptibility Mapping

MRIREAD: MRI Clinical Read

MRISERIAL: MRI Serial

MRI_INFARCTS: MRI Infarcts: 2021-01-29

NYUFDGHIP: NYU FDG-PET Hippocampus (pons normalized)

PETC3: PETC3

PETMETA3: FDG PET Scan Information

PETMETA_ADNI1: PET Scan Information

PETMETA_ADNIGO2: FDG PET Scan Information

PETQC: PET QC Tracking

PIBMETA: PIB Scan Information

PIBPETSUVR: U Pitt PIB PET Analysis

PIBQC: PIB QC Tracking

PICSLASHS: ASHS volume data

SPAP_AVID_FLORBETAPIR: sPAP Avid ADNI Florbetapir summaries

TAUMETA: Tau AV-1451 PET Scan Information

TAUQC: Tau AV-1451 PET QC

TBM22: Paul Thompson's Lab, Imaging Genetics Center (IGC), University of Southern California - Cross-sectional and longitudinal tensor-based morphometry Versions 2.0 and 2.1: 2020-03-17

TCV: Total Cranial Vault Segmentation

UASPMVBM: UA (Gene Alexander) MRI SPM voxel based morphometry (VBM) analysis

UCBERKELEYFDG_8mm: UC Berkeley - FDG analysis: 2023-02-17

UCBERKELEY_AMY_6MM: UC Berkeley - Amyloid PET 6mm Res analysis

UCBERKELEY_TAUPVC_6MM: UC Berkeley - Tau PET PVC 6mm Res analysis

UCBERKELEY_TAU_6MM: UC Berkeley - Tau PET 6mm Res analysis

UCD_ADNI1_WMH: Univerity of California Davis White Matter Hyperintensity Volumes (ADNI1)

UCD_WMH: UCD - White Matter Hyperintensity Volumes

UCSDVOL: Anders Dale Lab (UCSD) - Derived Volumes

UCSFASLFSCBF: ASL Perfusion CBF by FreeSurfer ROI

UCSFASLFS_V2: ASL Perfusion CBF by FreeSurfer ROI: 2015-11-02

UCSFASLQC: ASL Perfusion Raw QC

UCSFATRPHY: UCSF (Colin Studholme) Regional Atrophy Rates

UCSFFSL: Longitudinal FreeSurfer (FreeSurfer Version 4.4): 2016-02-01

UCSFFSL51: Longitudinal FreeSurfer (5.1) - Final Run w/ All A: 2022-03-01

UCSFFSL51ALL: Longitudinal FreeSurfer (5.1) - All Available Base Image: 2016-08-01

UCSFFSL51Y1: Longitudinal FreeSurfer (5.1) - Year 1 Base Image: 2016-08-01

UCSFFSX: Cross-Sectional FreeSurfer (FreeSurfer Version 4.3): 2015-11-02

UCSFFSX51: Cross-Sectional FreeSurfer (5.1): 2019-11-08

UCSFFSX51_ADNI1_3T: ADNI-1 3T Cross-Sectional FreeSurfer (5.1): 2016-02-01

UCSFFSX6: Cross-Sectional FreeSurfer (6.0)

UCSFFSX7: Cross-Sectional FreeSurfer (7.x)

UCSFSNTVOL: UCSF SNT Hippocampal Volumes

UPENNROI_MARS: UPENNROI_MARS: 2016-06-01

UPENNSPARE_AD: Spatial Pattern of Abnormalities for Recognition of Early AD (SPARE-AD). C. Davatzikos. U. Penn.: 2016-07-27

UPENNSPARE_MCI: Spatial Pattern of Abnormalities for Recognition of Early MCI to AD conversion (SPARE-MCI). C. Davatzikos. U. Penn.: 2016-08-12

UUCACIR: UU PET Analysis: 2016-07-18

Biospecimen

ALIQUOT_COUNT: Aliquot Count Table

APOERES: ApoE Genotyping - Results

BIOMARK: Biomarker Samples

BLENNOWPLASMANFL: Blennow Lab ADNI1 Plasma neurofilament light (NFL): 2018-10-03

BLENNOWPLASMANFLLONG: Blennow Lab ADNI1-2 Plasma neurofilament light (NFL) longitudinal: 2018-10-03

BLENNOW_LAB_CSF_GAP_21: BLENNOW_LAB_CSF_GAP_21

C2N_PRECIVITYAD2_PLASMA: C2N Diagnostics - PrecivityAD2 Blood Test Results for Aβ42/40 and p-tau217/np-tau217 ratios ADNI4

FNIHBC_BLOOD_BIOMARKER_TRAJECTORIES: Clinical Utility of Blood Biomarker Trajectories Study

FUJIREBIOABETA: Fujirebio Beta-Amyloid Ratio

FUJIREBIOABETAPLASMA: Plasma Amyloid Beta (1-42/1-40) Ratio Biomarker Feasibility Study - Fujirebio Lumipulse

GENETIC: ApoE Genotyping - Draw Data

JANSSEN_PLASMA_P217_TAU: ADNI 2_3 pilot_Janssen plasma p217+tau Simoa

LABDATA: Laboratory Data

LABTESTS: Clinical Laboratory Tests

LOCLAB: CSF - Local Lab Results

PLASMAABETA: Araclon Biotech S.L. ABtest40 and 42 Plasma Analysis

UGOTPTAU181: University of Gothenburg Longitudinal plasma P-tau181: 2020-06-18

UPENNBIOMKADNIDIAN2017: UPENNBIOMKADNIDIAN2017

UPENNBIOMK_MASTER: UPENN CSF Biomarker Master Alzbio3 (BATCH1-8)

UPENNBIOMK_ROCHE_ELECSYS: UPENN CSF Biomarkers Elecsys ADNI1,GO,2,3

UPENN_PLASMA_FUJIREBIO_QUANTERIX: UPENN - Plasma Biomarkers (Aβ42, Aβ40, ptau217, NfL, GFAP) measured by Fujirebio & Quanterix ADNI1,GO,2,3,4

URMC_LABDATA: ADNI3 URMC Lab Data

YASSINE_CSF: APOE glycosylation in ADNI CSF

batemanlab_20221118: BATEMANLAB_20221118

Neuropathology Results

NEUROPATH: NACC Neuropathology Data Form (Version 11)

Remotely Collected Datasets

Remotely collected data only avaliable in ADNI4 study phase

REMOTE_DATADIC: Remote Collected Data Dictionary Dataset

RMT_APOERES: ApoE Genotyping - Results

RMT_ECOG12PT: DIG Remotely administered Assessment of Everyday Cognition (Ecog) Questionnaire – Participant-Report Version

RMT_ECOG12SP: DIG Remotely administered Assessment of Everyday Cognition (Ecog) Questionnaire – Informant-Report Version

RMT_PTDEMOG: DIG Remotely administered participant demographics questionnaire

RMT_STORYTELLER: Novoic Storyteller Data

RMT_Screening: DIG Remotely administered screening questionnaire

Other Raw Datasets

DATA_DOWNLOADED_DATE: ADNI Study Data Downloaded Date

ADNI Derived Datasets

Derived datasets that are grenerated based on the package vignettes.

ADAE: [DERIVED] Analysis Dataset of Adverse Events

ADQS: [DERIVED] Analysis Dataset of Questionnaires

ADRS: [DERIVED] Response Analysis Dataset

ADSL: [DERIVED] Subject-Level Analysis Dataset

AE: [DERIVED] Derived Adverse Events

DERIVED_DATADIC: [DERIVED] Data dictionary for derived dataset

DM: [DERIVED] Derived Demographic Characteristics

GF: [DERIVED] Derived Genomics Findings

LB: [DERIVED] Derived Laboratory Test Results

METACORES: ADNI Metadata-Specs

NV: [DERIVED] Derived Nervous System Finding

QS: [DERIVED] Derived Questionnaires

RS: [DERIVED] Derived Clinical Classification

SC: [DERIVED] Derived Subject Characteristics

VS: [DERIVED] Derived Vital Signs

ADNI Specific Functions

Functions that are created specifically for the ADNI study data

Enrollment

get_adni_blscreen_dxsum(): Gets ADNI Baseline/Screening Diagnostics Summary

get_adni_enrollment(): ADNI Enrollment Date (Baseline Visit Date)

get_adni_screen_date(): Gets ADNI Screening Date

get_death_flag(): Death Flag

get_disposition_flag(): Study Discontinuation Flag

Study Protocol/Phase

adni_phase(): List ADNI Study Protocol/Phases

adni_phase_order_num(): ADNI Study Protocol Order

adni_pttype(): ADNI PTYPE

adni_study_track(): Get ADNI Study Track

convert_adni_phase_order_num(): Convert ADNI Study Phase Order Number

create_col_protocol(): Create COLPROT Column

original_study_protocol() create_orig_protocol(): ADNI Original Protocol Version

Data Dictionary

collect_value_mapping(): Collecting Coded Values for Multiple Variables

collect_value_mapping_single_var(): Collecting Variable Coded Values

convert_value_mapping(): Convert List Collected Coded Values

convert_value_mapping_phase_specific(): Convert List Collected Coded Values - PHASE Levels

datadict_as_tibble(): Convert `datadict_tbl` object into `tibble` object

extract_codelist_datadict(): Extract Codedlist from DATADIC

get_factor_fldname(): Gets Factor Field Name (FLDNAME)

get_factor_levels_datadict(): Gets Factor Levels from DATADIC Dataset

is_datadict_tbl(): Check `is_datadict_tbl` Object Class Type

set_datadict_tbl(): Set object to `datadict_tbl` class

convert_to_missing_value(): Convert Value into Missing Values

replace_values_dataset(): Replace Values for Multiple Variable - Wrapper

replace_values_phase_specific(): Replace Phase Specific Values for Single Variable

replace_values_single_var(): Replace Values for Single Variable Across Multiple Phase

create_usubjid(): Create USUBJID from RID and SITEID

Scoring Functions

compute_neurobat_subscore(): Scoring Function for NEUROBAT Sub-items

Utility Functions

Functions that can be used for general purpose

assert_non_missing(): Checks Missing Values

assert_uniq(): Checks Duplicated Values/Records

check_colnames(): Checks Column Name Exist

check_duplicate_records(): Checks Duplicated Records - Internal

check_is_logical(): Check A Boolean Value

convert_number_days(): Convert Number of Days

convert_to_missing_value(): Convert Value into Missing Values

detect_baseline_score(): Detect Closest Baseline Score

detect_decimal_value(): Detect Decimal Values

detect_numeric_value(): Detect Numeric Values

get_cols_name(): Extract Column Name

get_cols_value(): Get Columns With Specific Values

replace_multiple_values(): Replace/Substitute Multiple Values

split_strings(): Split Strings With Two Split Parameters