MRI data is one component of the comprehensive data set collected in ADNI participants. ADNI began in 2004 and to date 3 different phases of ADNI have been undertaken. The MR protocol evolved over these 3 phases. The MRI protocol for ADNI1 (2004-2009) focused on consistent longitudinal structural imaging on 1.5T scanners using T1- and dual echoT2-weighted sequences. One-fourth of ADNI 1 subjects were also scanned using essentially the same protocol on 3T scanners.

In ADNI-GO/ADNI2 (2010-2016), imaging was performed at 3T with T1-weighted imaging parameters similar to ADNI1. In place of the dual echo T2-weighted image from ADNI1, 2D FLAIR and T2*-weighted imaging was added at all sites. Both fully sampled and accelerated T1-weighted images were acquired in each imaging session. Advanced imaging was included depending on scanner manufacturer: diffusion imaging on GE scanners, resting state functional MRI on Philips scanners and arterial spin labeling on Siemens scanners.

ADNI 3 imaging is being done exclusively on 3T scanners. Nearly all of the imaging sequences from ADNI2 have been updated for inclusion in ADNI 3. Each of the ADNI 2 “advanced imaging” sequences is now included in the “basic” ADNI 3 protocol with a few site-wise exceptions related to sequence license issues.

In order to create imaging protocols that can be used to support drug studies, it is necessary to restrict the sequences employed to those commercially available on scanners.

ADNI users should be aware that there is a broad gap between older MRI systems and the state-of-the-art systems within each vendor’s product line. Thus, the ADNI MR data set includes a wide range of scanner platforms. A two-tiered approach is taken to accommodate the range of variability in scanners in ADNI 3. ‘ADNI 3 Basic’ and ‘ADNI 3 Advanced’ protocols have been created.

Both images and quantitative numeric ADNI MR data are available publically. All scans remain available for download by qualified users and are accessible via the Image Data Archive. The types of scans collected from each phase of the study are listed below. To view a full list of study data, review the data inventory page.

Quality Control

Each series in each exam undergoes quality control at Mayo Clinic. Two levels of quality control are performed; adherence to the protocol parameters and series-specific quality (i.e., subject motion, anatomic coverage, etc.). Scan quality is graded subjectively by trained analysts: 1-3 is acceptable and 4 is failure (unusable). This QC information will eventually be available for each series on LONI. Thus, users will be able to easily employ exam level QC information as filters in data collections.

SCANNER CHANGES

MR scanners routinely undergo upgrades. These can be relatively minor (SW version) or major (hardware changes, e.g. head coil). In some cases, the scanner itself will be replaced at an ADNI site. We advise the following approach to the issue of scanner changes:

1. Assume that longitudinal within subject data is not compatible before vs after a change in scanner.
2. Assume that longitudinal within subject data is not compatible before vs after a major hardware change e.g., change in head coil.
3. Assume that longitudinal within subject data maybe compatible before vs after a SW version change, but be advised that this may not be shown to be true eventually for some types of SW changes.

All technical scanner information is available in the DICOM headers, however this is not easily searchable at present (January 2018). Eventually, the relevant technical scanner information will be easily available and downloadable at the exam level for ADNI users at the time they create either image or numeric data collections. Thus users will be able to easily employ exam level technical scanner information as filters in data collections.

ADNI 2 TO 3 PROTOCOL COMPATIBILTY

Our approach to developing the ADNI 3 protocol was that the ADNI 3 protocol had to be modernized even if this introduced non-compatibility between ADNI 2 and ADNI 3 data for some series. Details are noted in the Series Types chart.

Recommended Image Data: Which scan to select?

For researchers interested in the imaging process as a whole, imaging files are available at every stage of pre- and post-processing. However, most researchers will prefer to use the scans that have undergone the maximum level of correction. These MPRAGE files are considered the best in the quality ratings and have undergone gradwarping, intensity correction, and have been scaled for gradient drift using the phantom data.

Read more about Standardized MRI Data Sets

Image Corrections Provided by ADNI

Mayo provided intensity normalized and gradient un-warped TI image volumes for all ADNI1 and many ADNI2 exams. As MR vendors offered these corrections online as part of the product, ADNI stopped performing its own preprocessing and instead employed the preprocessing performed by vendor product. Consequently, no offline TI image preprocessing is now needed and none is done in ADNI3.

Siemens scanners may save two variants of 3D scans with and without gradient inhomogeneity correction applied (gradwarp). Mayo QC will select the variant with gradwarp, but if users need to disambiguate these cases the gradwarp corrected version of the image will indicate “DIS3D” in the DICOM header field Image Type (0008,0008) for the series.

All T1 images include an on-scanner non-uniformity correction, this may not fully eliminate non-uniformity. Many volumetric analysis pipelines now include bias field correction, however users not using such a pipeline and performing analysis which may be influenced by non-uniform intensities within the image may wish to apply an additional bias field correction such as N4 (Tustison et al. IEEE TMI 2010, 29(6))

In the interest of promoting consistency in data analysis, a set of standardized MRI imaging data sets has been developed for the acquired 1.5T and 3T scans. Researchers are encouraged to utilize these complete data sets in their analysis and to reference them in reporting results. Doing so will help to support direct comparisons of various analysis methods. Details about the rationale and development of the standardized MRI data sets may be found in “Standardization of Analysis Sets for Reporting Results from ADNI MRI data“, Wyman BT et. al.

Standardized MRI Collections

Collections of uniformly pre-processed images corresponding with each of the standardized data sets have been created within the ADNI archive so that researchers may download the complete set of images quickly and efficiently. The collection names and descriptions are shown in the table below.

How to Download

For authorized ADNI users only:

Standardized Image Collections:

1. Log into the archive: https://ida.loni.usc.edu/login.jsp?project=ADNI
2. Under the DOWNLOAD menu, choose “Image Collections”
3. In the left navigation section, click “Other Shared Collections”
4. Select “ADNI”
5. Click on the collection name matching the desired standardized data set
6. Download to an appropriately named location on your computer system (i.e. ADNI1_Complete_Year_1)

Standardized Lists:

1. Log into the archive: https://ida.loni.usc.edu/login.jsp?project=ADNI
2. Under the DOWNLOAD menu, choose “Study Data”
3. In the left navigation, click “Study Info” then  “Data & Database”
4. Click on the link you wish to download (either ADNI 1.5T MRI Standardized Lists or ADNI 3T MRI Standardized Lists)
5. Download to an appropriately named location on your computer system (i.e. ADNI_3T_MRI_Standardized_Lists)