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ADNI T1w
Before anything, read and agree to the ADNI Data Use Agreement:
- DUA: https://adni.loni.usc.edu/wp-content/themes/adni_2023/documents/ADNI_Data_Use_Agreement.pdf
- Application portal: https://ida.loni.usc.edu/collaboration/access/appLicense.jsp
The application requires a brief research statement.
Timeline: Approval took less than a week.
| Phase | Years | Scanner | Notes |
|---|---|---|---|
| ADNI 1 | 2004–2009 | 1.5T (main), 3T (~25%) | T1 + dual-echo T2 |
| ADNI GO | 2010–2011 | 3T | Bridge between ADNI 1 and 2 |
| ADNI 2 | 2011–2016 | 3T | Added FLAIR, T2*, accelerated T1s |
| ADNI 3 | 2016–2021 | 3T | Added DTI, ASL, fMRI at all sites |
| ADNI 4 | 2022–present | 3T | Currently enrolling |
Collections of preprocessed images are provided by default. To access raw scans you must create your own "collection"
Warning: All data with PTIDs matching the format
381_S_10###have been removed due to serious quality concerns. Do not use these in any analysis. See: https://adni.loni.usc.edu/news-publications/adni-data-advisory/
After login, the main interface is at https://ida.loni.usc.edu. Select ADNI as your project.
- Search & Download → Image Collections: For downloading imaging data (T1s, DWI, FLAIR, etc.)
- Search & Download → Study Data / Study Files: For tabular/clinical CSV data
- Search & Download → ARC Builder: Newer interface for tabular data — explore variables, build cohorts, download CSVs. Not used for imaging.
Under Image Collections → Data Collections → Other Shared Collections → ADNI, there are pre-built collections like "ADNI1:Baseline 3T", "ADNI1:Complete 1Y 1.5T", etc.
Go to Search & Download → Image Collections → Advanced Search tab.
Set the following filters:
| Filter | Setting |
|---|---|
| Image Types | Original only (leave Pre-processed and Post-processed unchecked) |
| Project/Phase | ADNI 1, ADNI GO, ADNI 2, ADNI 3, ADNI 4 (select as needed) |
| Modality | MRI |
| Acquisition Type | 3D |
| Weighting | T1 |
On the Image Description field: You can use *RAGE* as a wildcard filter to get all the MPRAGE (MP-RAGE) scans.
- T1 + 3D + all descriptions: ~32,018 items
- T1 + 3D + MPRAGE only: ~14,909 items
The results will contain multiple series per subject per visit. For example, a single visit may have:
-
MPRAGE(non-accelerated) -
MPRAGE GRAPPA2(accelerated) Accelerated Sagittal MPRAGE
All are "Original" type. You will need to deduplicate after download, using QC files (see Section 6).
- From the Advanced Search Results tab, click Select All
- Click Add to Collection and give it a descriptive name (e.g.,
adni_all_t1_mprage_3d) - Go to the Data Collections tab to manage and download your collection
Click Advanced Download (top right of the Data Collections view).
The IDA Advanced Download page provides URLs that can be fed into a download manager. This is the best approach for large collections.
IDA-tested download managers:
| Tool | Platforms | Site |
|---|---|---|
| jDownloader | Linux, Mac, Windows | https://jdownloader.org |
| Uget | Linux, Windows | https://ugetdm.com |
| FDM | Mac, Windows | https://freedownloadmanager.org |
Workflow: Advanced Download → copy the zip URLs → paste into your download manager.
LONI provides an IdaDownloader jar file (found on the IDA support/download page). As of May 2026 the file is IdaDownloader_15May2026.jar.
Caveat: It requires Oracle Java. It will refuse to run on Ubuntu's OpenJDK.
Or if your HPC has modules:
module avail java
module load java/oracle-21 # or whatever Oracle JDK is available
java -jar IdaDownloader_15May2026.jarStatus: Not yet tested as of this writing, needs further investigation.
If the above don't work, fall back to the browser. Use Chrome, Edge, or Firefox.
Important constraints:
- Same computer, same IP address for the entire download session
- Sessions time out on inactivity don't let your machine sleep
- Static IP required
- browser page needs to stay open
Tested and confirmed the following do not work:
-
curlwith the download URLs directly, stalls at 0 bytes -
curl -b cookies.txtwith exported Firefox cookies (via cookies.txt addon)
Downloads are in Zip64 format.
Images download as DICOM files in a deeply nested folder structure:
ADNI/
├── 001_S_XXXX/
│ ├── MPRAGE/
│ │ └──DATE/
│ │ └── SXXXXX/
│ │ └── *.dcm
│ ├── Accelerated_Sagittal_MPRAGE/
│ │ └── ...
├── 002_S_XXXX/
│ └── ...You will need dcm2niix to convert DICOM to NIfTI:
Search & Download → ARC Builder
Workflow: explore variables → build cohorts with filters → download.
With raw downloads, you'll have multiple scans per subject per visit. To select the best one:
-
Preferred scan: Check
MAYOADIRL_MRI_IMAGEQCfor the flagged "preferred" scan per visit -
Quality rating: Use
MRIQUALITY.csv— ratings 1–3 are acceptable, 4 is failure/unusable - Fallback: If no QC data exists, use the first (or most recent) scan for that visit
For ADNI 4, use the "chosen" series selected during Mayo ADIR Lab QC.
The Clinica converter (https://aramislab.paris.inria.fr/clinica/docs/public/dev/Converters/ADNI2BIDS/) is the most established tool, but as of May 2026:
- Not updated for the new LONI interface (broken since the Sept 2024 refactor)
- Does not support ADNI 4
- The Clinica team is waiting for the interface to stabilize before updating
- Discussion: https://groups.google.com/g/clinica-user
Without Clinica, the workflow is:
- Download raw DICOMs (Section 4) and clinical CSVs (Section 5)
- Use QC files to select one scan per subject per visit (Section 6)
- Convert selected DICOMs to NIfTI with
dcm2niix - Organize into BIDS directory structure:
bids/bash
├── participants.tsv
├── sub-ADNI001SXXXX/
│ ├── ses-YYY/
│ │ └── anat/
│ │ ├── sub-ADNI001SXXXX_ses-YYY_T1w.nii.gz
│ │ └── sub-ADNI002SXXXX_ses-YYY_T1w.json
│ ├── ses-ZZZ/
│ │ └── ...
| Resource | URL |
|---|---|
| ADNI main site | https://adni.loni.usc.edu |
| IDA login | https://ida.loni.usc.edu/login.jsp?project=ADNI |
| Data Use Agreement | https://adni.loni.usc.edu/wp-content/themes/adni_2023/documents/ADNI_Data_Use_Agreement.pdf |
| MRI overview | https://adni.loni.usc.edu/data-samples/adni-data/neuroimaging/mri/ |
| MRI preprocessing docs | https://adni.loni.usc.edu/data-samples/adni-data/neuroimaging/mri/mri-pre-processing/ |
| Data advisory (bad PTIDs) | https://adni.loni.usc.edu/news-publications/adni-data-advisory/ |
| ADNI Data User Guide | https://adni.loni.usc.edu/help-faqs/adni-data-user-guide/ |
| Clinica converter docs | https://aramislab.paris.inria.fr/clinica/docs/public/dev/Converters/ADNI2BIDS/ |
| Clinica user group | https://groups.google.com/g/clinica-user |
| FAQs | https://adni.loni.usc.edu/help-faqs/faqs/ |
| IDA User Manual (PDF) | https://ida.loni.usc.edu/explore/jsp/support/IDA_User_Manual.pdf |
| IDA Support / FAQ | https://ida.loni.usc.edu/explore/jsp/support/support.jsp |