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MRI Acquisition

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.

Acquisition Table

ADNI1
(1.5T Scanner)
ADNI GO/2
(3T Scanner)
ADNI 3
Participant Scan:

  1. Localizer
  2. MP-RAGE
  3. MP-RAGE – REPEAT
  4. B1 Calibration – Head Coil (if applicable)
  5. B1 Calibration – Body Coil (if applicable)
  6. T2 Dual Echo (Straight Axial – cover below cerebellum through top of head)
Participant Scan:

  1. Localizer
    1a. Calibration/Reference Scan (if applicable)
  2. Sagittal MP-RAGE/IR-SPGR
  3. Accelerated Sagittal MP-RAGE/IR-SPGR
  4. Resting State fMRI (Philips Systems Only) – Subjects should have eyes OPEN.
  5. Axial T2-FLAIR
  6. Axial T2-Star
  7. Axial ASL Perfusion (Siemens Systems Only) – Subjects should have eyes OPEN.
  8. Axial DTI Scan (GE Systems)
Participant Scan:

  1. 3 Plane Localizer
  2. Accelerated Sagittal MPRAGE
  3. Sagittal 3D FLAIR
  4. Axial T2 STAR
  5. Axial 3D PASL (Eyes Open)
  6. Axial DTI
  7. Field Mapping
  8. Axial rsfMRI (Eyes Open)
  9. HighResHippocampus
Phantom Scan:

  1. Localizer
  2. MP-RAGE (with slice thickness increased to cover phantom)
  3. MP-RAGE – REPEAT (same as above)
  4. B1 Calibration – Head Coil (if applicable)
  5. B1 Calibration – Body Coil (if applicable)
  6. T2 Dual Echo (Straight Axial – Through center of phantom)
  7. MP-RAGE CORONAL (with slice thickness increased to cover phantom)
Phantom Scan:

  1. Localizer 1a. Calibration/Reference Scan (if applicable)
  2. QC Phantom MP-RAGE/IR-SPGR (Accelerated)
  3. QC Phantom fMRI (Philips Systems)
Phantom Scan:

  1. 3 Plane Localizer
  2. QC Phantom MPRAGE
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.

Series Type

3D T1

Spatial resolution was improved slightly in ADNI 3 to 1mm cubed. We believe this should not have a dramatic effect on longitudinal within person analyses.

FLAIR

Changed from 2D to 3D in ADNI 3. This introduces a significant improvement in spatial resolution plus a change in the contrast model. It is doubtful that this data type will be consistent from ADNI 2 to ADNI 3 without significant data processing to account for the change in acquisition.

T2* GRE

No change from ADNI 2 to ADNI 3 for GE or Philips scanners. A 3-echo train GRE sequence is acquired on Siemens scanners with phase and magnitude volumes saved for each echo. This will allow creation of pseudo quantitative susceptibility maps. The magnitude 20ms volume (3rd echo), from these Siemens GRE acquisitions is compatible with GRE scans acquired in ADNI GO/2.

Hi resolution coronal for hippocampal subfields – little change, should be compatible from ADNI 2 to ADNI 3

ASL

2D PASL was used in ADNI 2 and 3D (PASL or pCASL) are used wherever possible in ADNI 3. Thus this data t ype is unlikely to be compatible between ADNI 2 and ADNI 3.

DTI

ADNI 3 uses 2.0 mm isotropic voxels, but ADNI 2 used 2.7 mm, with b = 0 and 1000 s/mm2 weighted volumes. ADNI3 Basic and Advanced both provide b = 0 and 1000 s/mm2 weighted volumes, but the b = 500 and 2000 s/mm2 volumes of Advanced would have to be excluded before comparison with ADNI 2.

fMRI

The basic version of each of these should be fairly compatible, but the advanced ADNI 3 version will not be compatible with ADNI 2 data

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

MRI Pre-Processing

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))

ADNI1 AND ADNI2/GO

Each MPRAGE image in the database at LONI is linked with related image files, which have undergone specific image pre-processing correction steps. These corrections are as follows:

1. Gradwarp: gradwarp is a system-specific correction of image geometry distortion due to gradient non-linearity. The degree to which images are distorted due to gradient non-linearity varies with each specific gradient model. We anticipate that most users will prefer to use images which have been corrected for gradient non-linearity distortion in analyses.

2. B1 non-uniformity: this correction procedure employs the B1 calibration scans noted in the protocol above to correct the image intensity non-uniformity that results when RF transmission is performed with a more uniform body coil while reception is performed with a less uniform head coil.

3. N3: N3 is a histogram peak sharpening algorithm that is applied to all images. It is applied after grad warp and after B1 correction for systems on which these two correction steps are performed. N3 will reduce intensity non-uniformity due to the wave or the dielectric effect at 3T. 1.5T scans also undergo N3 processing to reduce residual intensity non-uniformity.

The need to perform the image pre-processing corrections outlined above varies with manufacturer and system RF coil configuration. Philips Systems were equipped with B1 correction as product at the time ADNI began. In addition, Phillips gradient systems tend to be linear. Therefore, no gradwarped and no B1 corrected pre-processed files are generated for images acquired on Phillips Systems. The files available by manufacturer will be:

Phillips Systems:
  1. Raw DICOM
  2. N3 corrected
GE and Siemens systems with transmit-receive head RF coils:
  1. Raw DICOM
  2. Gradwarped
  3. Gradwarp plus N3
GE and Siemens systems with receive-only head RF coils:
  1. Raw DICOM
  2. Gradwarped
  3. Gradwarp plus ADNI1 only plus N3

As noted above, it is anticipated that nearly every user will prefer to employ scans which have undergone gradwarp correction in analyses. Users who have developed their own set of tools for image intensity corrections may wish to simply use the gradwarped files. However, it is anticipated that most users will want to use the fully pre-processed files. These are most easily identified as files that contain N3 in the identifier. Note that these corrections are applied only to T1 Weighted (not FSE) images, and as outlined below, only to the one T1 Weighted volume associated with each time point that has been designated as “best” by the ADNI quality assurance team.

Phantom-based scaling measures

In addition to the corrections outlined above, phantom-based measures of spatial scaling are associated with each MPRAGE image in an accompanying XML file. A version of the image with these spatial scale factors applied will be provided. Recall that each ADNI human exam is followed immediately by an acquisition with the ADNI phantom. Absolute scaling along each of the cardinal axes (x, y, z) is measured with the phantom. These phantom-based measurements can be used to retrospectively scale the accompanying human MPRAGE image. In the limit that the image matrix is aligned with the cardinal axes, this amounts to adjusting the voxel size. For images for which this does not hold, application of the scale factors is slightly more complicated, as scaling along one axis in the magnet will be mixed into the other two dimensions by the oblique rotation.

Standardized MRI Data Sets

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.

ADNI1 Standardized Data Collections

ADNI 1 Standardized Data Collections for 1.5T scans
Collection Name Collection Description
ADNI1:Screening 1.5T Subjects who have a screening scan
ADNI1:Complete 1Yr 1.5T Subjects who all have screening, 6 and 12 month scans
ADNI1:Complete 2Yr 1.5T Subjects who have screening, 6 months, 1 year, 18 months (MCI only) and 2 year scans
ADNI1:Annual 2 Yr 1.5T Subjects who have screening, 1, and 2 year scans
ADNI1:Complete 3Yr 1.5T Subjects who have screening, 6 months, 1 year, 18 months (MCI only), 2, and 3 year (normal and MCI only) scans
ADNI 1 Standardized Data Collections for 3T scans
Collection Name Collection Description
 ADNI1:Baseline 3T Subjects who have a screening scan
ADNI1:Complete 1Yr 3T Subjects who all have screening, 6 and 12 month scans
ADNI1:Complete 2Yr 3T Subjects who have screening, 6 months, 1 year, 18 months (MCI only) and 2 year scans
ADNI1:Annual 2 Yr 3T Subjects who have screening, 1, and 2 year scans
ADNI1:Complete 3Yr 3T Subjects who have screening, 6 months, 1 year, 18 months (MCI only), 2, and 3 year (normal and MCI only) scans
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)