ADNI

The MRI Core developed structural MRI protocols and an MRI phantom for calibration. MRI scanner protocols are available for GE, Philips and Siemens devices.

MRI Technical Procedures Manual

The MRI Technical Procedures Manual covers Site Qualification, MRI Subject Pre-Scan Procedures, MRI Subject Scan Protocol, MRI Subject Scan Procedures, MRI Subject Scan Procedures and related forms.

• MRI Technical Procedures Manual
• MRITrainingManual-ADN_A4B28.pdf

Related Documentation
• ADNI MRI Core Protocol Selection Summary
• ADNI MRI Method for Non-ADNI Studies

MRI Acquisition | MRI Scanner Protocols | MRI Quality Control | MRI Pre-processing

MRI Acquisition

Average Scanning Session

The ADNI exam consists of the following imaging sequences:

Subject Scan

1. Localizer/Scout Scan (20 secs)
2. Straight Sagittal 3D MPRAGE (8-10 mins)
3. Straight Sagittal 3D MPRAGE – REPEAT – (8-10 mins)
4. B1 Calibration Scan Phase Array Coil (if applicable) (30 secs)
5. B1 Calibration Scan Body Coil (if applicable) (30 secs)
6. Axial Dual Echo T2 FSE (5 mins)

ADNI Phantom – Quality Control Scans (following subject scan)

1. Localizer/Scout Scan (20 secs)
2. Straight Sagittal 3D MPRAGE (8-10 mins)

The MPRAGE is the T1-weighted 3D series which will be used for most morphometric analyses. Two identical MPRAGE scans are done in each patient study back to back. The purpose of this is to maximize the probability that at least one high quality MPRAGE scan is obtained at each examination, and minimize the probability that subjects will need to return for a repeat study because of suboptimal image quality. The B1-calibration scans are obtained to correct for image intensity inhomogeneity due to receiver coil non uniformity, as described below, and would not be useful to the typical user. The dual fast spin echo (FSE) series a T2/proton density scan is obtained for pathology detection.

MRI Scanner Protocols

MRI Scanner Protocols from recent models of General Electric (GE) Healthcare, Philips Medical Systems, and Siemens Medical Solutions are supported. The tables below contain active links to PDF files of scanner protocols, click to download.

ADNI GO / ADNI 2 (3T)

For Related, Non-ADNI Studies

ADNI 1

View the ADNI 1 Protocols

MRI Acquisition | MRI Scanner Protocols | MRI Quality Control | MRI Pre-processing | Back to Top

MRI Quality Control

Use of image quality rating data in ADNI

Each exam undergoes a quality control evaluation at Mayo Clinic. Exams are evaluated for the presence of structural abnormalities that may affect inclusion/exclusion from the study at the time of baseline screening evaluation. Obviously, if a subject appears in the LONI data base, he/she has passed inclusion criteria. For example, the presence of white matter disease is not an exclusionary criteria for ADNI, but users may want to restrict download of scans to those which have little or no white matter disease. Users may want to reference the quality control results contained in the clinical download files when selecting scans for download based on presence or absence of certain abnormities on MRI.

The MRI quality control files also contains scan quality ratings. The presence, absence and severity of common artifacts (e.g. blurring due to head motion) is indicated. Contrast to noise and intensity homogeneity (after the ADNI corrections listed above) are also graded. Users may want to restrict download of scans to those which meet certain quality criteria. Using the criteria provided in the QC files, users can choose scans which met any desired set of image quality criteria for download from the MRI data base.

Finally, recall that back-to-back MPRAGE scans are acquired on each subject. The final step in scan grading is designation of one MPRAGE as “the” scan recommended for use. In the event of a repeat exam for a particular time point due to image quality problems, one of the four possible MPRAGE scans acquired is designated as “the” best MPRAGE for that particular time point. The ADNI preprocessing steps outlined above are applied only to the one MPRAGE designated as “best” at each time point. Obviously, the user can select whichever scan is desired, but it is anticipated that the scan selected as best at each time point by the ADNI MRI quality assurance team would be most useful to typical users.

Recommended Image Data: Which scan to select?

For the sake of completeness, the various files with different levels of pre-processing correction above are available to all users. However, it is envisioned that most users would want to use the scans that have undergone the maximum correction in their analyses. This file will be the MPRAGE that has been identified as “best” in the quality ratings, and undergone gradwarping, intensity correction, and has been scaled for gradient drift using the phantom data. This will be identifiable as the file with “N3″ and “scaled” in the file name.

MRI Acquisition | MRI Scanner Protocols | MRI Quality Control | MRI Pre-processing | Back to Top

MRI Pre-Processing

Image Corrections Provided by ADNI

Each MPRAGE image in the database at LONI is linked with related image files which have undergone specific image preprocessing 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. It is anticipated that most users would want 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 which 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 preprocessing corrections outlined above does vary 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 preprocessed files are generated for images acquired on Phillips Systems. The files available by manufacturer will be:

Phillips Systems:

1. unpreprocessed DICOM
2. N3 corrected

GE and Siemens systems with transmit-receive head RF coils:

1. unpreprocessed DICOM
2. gradwarped
3. gradwarp plus N3

GE and Siemens systems with receive-only head RF coils:

1. unpreprocessed DICOM
2. gradwarped
3. gradwarp plus B1 plus N3

As noted above it is anticipated that nearly every user would want to employ scans which have undergone gradwarp correction in analyses. Users that 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 which contain N3 n the identifier. Note that these corrections are applied only to MPRAGE images (not FSE), and as outlined below only to the one MPRAGE 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 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.

Masks

Masks created by the MR Core as part of preprocessing are useful for performing N3 correction and are not brain masks. Therefore, the description of these masks has been updated to read “Intracranial Space” rather than “Brain.”

MRI Acquisition | MRI Scanner Protocols | MRI Quality Control | MRI Pre-processing | Back to Top