Brain Morphometry Imaging Protocols

The Morphometry BIRN provides optimized imaging protocols for both structural and diffusion tensor imaging (DTI) experiments. These protocols are based on studies conducted within mBIRN which looked at reliability and reproducibility of derived data measures when scanning parameters and image signal-to-noise ratio are varied.

Structural (T1-weighted scans)

In the case of structural imaging, “optimization” refers to generating sufficient gray / white matter contrast in T1-weighted images so that one can achieve accurate, reliable results for brain structures using the FreeSurfer and other processing packages. The FreeSurfer recommended protocol is here.

In addition, mBIRN researchers have worked with the Alzheimers Disease Research Initiative to define structural brain MRI protocols. The protocols for a wide range of scanners can be found here.

Diffusion Tensor Imaging Protocol

In the case of diffusion tensor imaging, “optimization” of the protocol depends upon the brain structure of interest. In general, the lower the fractional anisotropy (FA) in a given region, the more scan-time units will be needed to accurately calculate the FA. The Johns Hopkins University MBIRN site has performed DTI calibration studies to identify salient issues in DTI data acquisition. They discuss the amount of DTI data needed to resolved certain brain structures in terms of  the “scan-time unit”, which is defined as a single run consisting of 5 b=0 scans, and 30 diffusion-weighted directions with a single average.  This work is discussed in:

Farrell JA, Landman BA, Jones CK, Smith SA, Prince JL, van Zijl PC, Mori S.  Effects of signal-to-noise ratio on the accuracy and reproducibility of diffusion tensor imaging-derived fractional anisotropy, mean diffusivity, and principal eigenvector measurements at 1.5 T.  J Magn Reson Imaging. 26(3):756-67 (2007).

That study found that 3 scan-time units are sufficient for good accuracy and reliability of DTI measurements for a usual set of brain structures. That means that you can either repeat a 5 b=0, 30-direction DTI scan 3 times or repeat a 3 b=0, 15-direction DTI scan 6 times. Note that in the latter example, the number of b=0 images is close, but not identical to the former case since you cannot specify half of a scan.  However, note that repeating scans with a smaller number of directions may bias your diffusion measurement.  The conditions under which this can occur is discussed in:

Bennett A. Landman, Jonathan A.D. Farrell, Craig K. Jones, Seth A. Smith, Jerry L. Prince, and Susumu Mori, Effects of diffusion weighting schemes on the reproducibility of DTI-derived fractional anisotropy, mean diffusivity, and principal eigenvector measurements at 1.5T, NeuroImage 36:1123-1138 (2007).

A protocol to acquire data of this type is:

  • Five b=0 acquisitions / scan  (Note that b = 0 is shorthand – the actual choice should be b = 30-100 s/mm2, so the issue of flow attenuation and primer-crusher behavior of the diffusion gradients are addressed.)
  • Two b-values; b = 30-100 and b = 700 – 1000 s/mm2
  • TR = shortest to accommodate all slices, typically 8 – 14 sec
  • TE = min for full acquisition (note that it is a good idea to add 4 – 8 msec to the minimum TE value as the minimum values can result in duty cycle related errors on some scanners)
  • Number of slices = minimum needed to cover entire brain including the cerebellum (55-60)
  • Orientation = axial
  • Slice thickness = 2.0 mm
  • Slice gap = 0 mm
  • FOV = 240 mm
  • Matrix size = 96 x 96  (Resulting in 2x2x2 mm3 isotropic voxels)
  • 3 data sets per subject
  • No zero filling or interpolation
  • k-space coverage = full k=space coverage (symmetric)
  • Parallel imaging: SENSE (p = 2) for Philips and GRAPPA for Siemens
BIRN is supported by NIH grants 1U24-RR025736, U24-RR021992, U24-RR021760 and by the Collaborative Tools Support Network Award 1U24-RR026057-01.