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ADNI Dataset Preprocessing

  • To access ADNI dataset, please first visit ADNI website: https://adni.loni.usc.edu/ and apply for data access here: https://ida.loni.usc.edu/collaboration/access/appApply.jsp?project=ADNI.
  • Once you get an access, login to IDA and dowlonad necessary files for each modality.
  • In essence, for each data modality, please (1) download the neceesary files and (2) run preprocessing code.
  • Please note the date on downloaded file name would be changed based on your downloading date. Thus, update the date in each preprocessing file followingly.

0. Diagnosis Data

Data Folder

data/
├── adni
    └── diagnosis
        └── DXSUM_PDXCONV_22Apr2024.csv

Steps

  1. Search & Download -> ARC Builder, Search DXSUM and add it to collections.
  2. Downloads -> Tables, download DXSUM
  3. Place the file under /data/adni/diagnosis/

1. Image (MRI) Preprocessing

Data Folder

data/
├── adni
    └── image
        └── {Subject ID}_{Scan date}
        └── {Subject ID}_{Scan date}
        └── ...

Steps

  1. Search & Download -> Image Collections, Search without Subject ID and save files as {Subject ID}_{Scan date} format.
  2. Build CBICApipeline container using file: image/CBICApipeline_centos7.def
  3. Define singularity wrapper file: image/singularity_wrapper.sh
  4. Define configuration file: image/config_3.5D.sh
  5. Submit jobs using file: image/ADNI_3.5D_2020_SubmitProcessingPipeline.sh
  6. Run python file: image/GetADNI_Ravens.py

2. Genomic Preprocessing

Data Folder

data/
├── adni
    └── genomic
        └── ADNI_cluster_01_forward_757LONI.bim
        └── ADNI_cluster_01_forward_757LONI.bed
        └── ADNI_cluster_01_forward_757LONI.fam
        └── ADNI_GO_2_Forward_Bin.bim
        └── ADNI_GO_2_Forward_Bin.bed
        └── ADNI_GO_2_Forward_Bin.fam
        └── ADNI_GO2_GWAS_2nd_orig_BIN.bim
        └── ADNI_GO2_GWAS_2nd_orig_BIN.bed
        └── ADNI_GO2_GWAS_2nd_orig_BIN.fam
        └── ADNI3_PLINK_Final.bim
        └── ADNI3_PLINK_Final.bed
        └── ADNI3_PLINK_Final.fam
        └── ADNI3_PLINK_FINAL_2nd.bim
        └── ADNI3_PLINK_FINAL_2nd.bed
        └── ADNI3_PLINK_FINAL_2nd.fam

Steps

  1. Search & Download -> Genetic Files -> Downloads, search below files and download
    • ADNI 1 SNP genotype data - PLINK
    • ADNI GO/2 SNP genotype data - Complete PLINK for sets 1 - 9
    • ADNI GO/2 SNP genotype data - Complete PLINK for sets 10 - 15
    • ADNI3 SNP genotype data Set 1 - PLINK
    • ADNI3 SNP genotype data Set 2 - PLINK
  2. Unzip each file and place the unziped files (file name will match with above files) .bim, .bed, .fam files under /data/adni/genomic/
  3. Move to data/adni/biospecimen and follow step-by-step at genomic/genomic_preprocess.ipynb

3. Clinical Preprocessing

Data Folder

data/
├── adni
    └── clinical
        └── MEDHIST_09May2024.csv
        └── NEUROEXM_09May2024.csv
        └── PTDEMOG_09May2024.csv
        └── RECCMEDS_09May2024.csv
        └── VITALS_09May2024.csv

Steps

  1. Search & Download -> ARC Builder, Search below files, add them into collections and download.
    • MEDHIST
    • NEUROEXM
    • PTDEMOG
    • RECCMEDS
    • VITALS
  2. Unzip each file and place the unziped files under /data/adni/clinical/
  3. Move to /data/adni/clinical and run clinical/clinical_preporcess.py

4. Biospecimen Preprocessing

Data Folder

data/
├── adni
    └── biospecimen
        └── APOERES_09May2024.csv
        └── UPENNBIOMK_ROCHE_ELECSYS_09May2024.csv

Steps

  1. Search & Download -> ARC Builder, Search below files, add them into collections and download.
    • APOERES
    • UPENNBIOMK_ROCHE_ELECSYS
  2. Unzip each file and place the unziped files under /data/adni/biospecimen/
  3. Move to /data/adni/biospecimen and run biospecimen/biospecimen_preprocess.py