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  • Anatomical Imaging Scan - T2- weighted, 3-D fast spin-echo sequence
    • This scan is used for optimizing the gray/white matter contrast, which is required for registration and analysis.
    • Current Parameters:  Cylindrical acquisition of k-space, with a TR of 350 ms, and TEs of 12 ms per echo for 6 echoes, field-of-view of 20 x 20 x 25 mm3 and matrix size = 504 x 504 x 630 giving an image with 0.040 mm isotropic voxels.  Total imaging time is currently ~14 hours.
  • Diffusion Tensor Imaging - 3D Diffusion Weighted Fast Spin-Echo sequence
    • This scan is used for calculating differences in the tissue microstructure, particularly the white matter.
    • Current Parameters: Echo train length of 6 will be used, with a TR of 270 ms, first TE of 32 ms, and a TE of 10 ms for the remaining 5 echoes, one average, field-of-view 14 x 14 x 25 mm3 and a matrix size of 180 x 180 x 324 yielding an image with 0.078 mm isotropic voxels.  Five b=0 s/mm2 images and 30 high b-value images (b=1917 2147 s/mm2) in 30 different directions were acquired, using the Jones30 scheme (Jones et al. Magnetic Resonance in Medicine, 1999).  Total imaging time is currently ~12 hours.
  • P7 Brain scan - Diffusion Tensor Imaging - Used for Gray/White Matter contrast in young brains.
    • This scan was needed to enhance the gray/white matter contrast at the younger ages prior to large scale myelination.
    • This diffusion sequence is a 3D diffusion-weighted FSE, with TR= 270 ms, echo train length = 6, first TE = 30 ms, TE = 10 ms for the remaining 5 echoes, one average, FOV = 25 mm × 14 mm × 14 mm, and a matrix size of 450 × 250 × 250, which yielded an image with 56 µm isotropic voxels.  One b=0 s/mm2 image is acquired and 6 high b-value (b = 2147 s/mm2) images were acquired at the following directions (1,1,0), (1,0,1), (0,1,1), (-1,1,0), (-1,0,1) and (0,1,-1) corresponding to (Gx,Gy,Gz).  Total imaging time was ~ 14 hours. 

    • After the scan is complete, the high b-value images are averages to create a diffusion weighted image that has acceptable contrast for the image registration pipeline.

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