Test-retest Diffusion MRI, measured at 1.5 mm isotropic resolution, b-value=2000 s/mm^2

MRI Measurements were conducted on 6 healthy male participants (ages: 27-40), who provided informed consent, according to a protocol approved by the Stanford University Institutional Review Board.

MRI data were collected at the Center for Cognitive and Neurobiological Imaging at Stanford University on 3T GE Discovery MR750 MRI system. A 32-channel head coil was used. A twice-refocused spin echo diffusion-weighted sequence was used. The spatial resolution of the measurement was 1.5x1.5x1.5 mm^3. 96 diffusion-weighting directions were used, with a b-value was used: 2000 s/mm^2 (TE=96.8 msec). 10 b=0 images were acquired at the beginning of each scan. Two repeated sets of images were acquired in immediate succession. To mitigate the effects of EPI spatial distortions, measurements of the B0 magnetic field were performed. Field maps were collected in the same slices as the DWI data using a 16 shot, gradient echo spiral trajectory pulse sequence. Two volumes were successively acquired, one with TE set to 9.091 ms and one with TE increased by 2.272 ms, and the phase difference between the volumes was used as an estimate of the magnetic field. To track slow drifts in the magnetic field (e.g., due to gradient heating) field maps were collected before and after the DWI scans and between successive DWI scans.

The B0 field maps were smoothed in space and time using local linear regression and then used to guide multifrequency reconstruction of the spiral-based functional volumes and unwarping of the EPI-based functional volumes. The reconstructed MR images were motion corrected to the average b=0 image in each scan, using a rigid body alignment algorithm, implemented in SPM (http://www.fil.ion.ucl.ac.uk/spm/). The direction of the diffusion-gradient in each diffusion-weighted volume was corrected using the rotation parameters from the motion correction procedure. Because of the relatively long duration between the RF excitation and image acquisition in the twice-refocused spin echo sequence used, there is sufficient time for eddy currents to subside. Hence, eddy current correction was not applied. All pre-processing steps have been implemented in Matlab as part of the vistasoft software distribution which can be downloaded at http://github.com/vistalab/vistasoft.