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 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.”