Micro-diffusion tensor imaging

In this paper“Filopodia are required for cortical neurite initiation : Nature Cell Biology”, I found a new MRI based imaging method muDTI. Very interesting. Although I still not totally understand how it works.

method section about muDTI

Before imaging, Bouin’s-fixed embryos were washed in PBS for more than 24 h to remove the fixation solution and transferred into home-built magnetic resonance-compatible tubes. The tubes were then filled with fomblin (fomblin profludropolyether; Ausimont, Thorofare, NJ) to prevent dehydration.

Imaging was performed using an 11.7 Tesla spectrometer with microimaging gradient (300 Gauss cm-1 maximum). A saddle coil (10 mm diameter; Bruker Biospin, Billerica, MA) was used as both the radio frequency signal transmitter and receiver33. The MRI sequence was based on a three-dimensional fast-echo sequence with navigator-echo phase-correction scheme and segmented k-space acquisition with an echo-train length of four. Three-dimensional diffusion-weighted images were acquired with a repetition time of 0.9 s, an echo time of 25 ms and four signal averages. The field of view was 16 mm times 9 mm times 9 mm and the native imaging resolution was approximately 0.09 mm times 0.09 mm times 0.09 mm. At least six diffusion-weighted images with b values of 1000–1200 s mm-2 were acquired. Diffusion sensitizing gradients were applied along six different orientations: [0.707, 0.707, 0], [0.707, 0, 0.707], [0, 0.707, 0.707], [-0.707, 0.707, 0], [0.707, 0, -0.707], [0, -0.707, 0.707]. We also acquired at least one image with a b value of 150 s mm-2. The imaging time for muDTI was approximately 20 h.

The diffusion tensor was calculated using a multivariate linear fitting method, and three pairs of eigenvalues and eigenvectors were calculated for each pixel. The eigenvector associated with the largest eigenvalue was referred to as the primary eigenvector. For the quantification of anisotropy, fractional anisotropy was used. Colour-map images were generated by combining the images of primary eigenvector and fractional anisotropy into red–green–blue (RGB) images. In the colour map images, the ratio between RGB components in each pixel was defined by the ratio of the absolute values of x, y and z components of the primary eigenvector, and the intensity was proportional to the fractional anisotropy. Red was assigned to the anterior–posterior axis, green to the medial–lateral axis, and blue to the superior–inferior axis.