3t allegra head only scanner

Diffusion data were acquired on a Siemens 3T Allegra head-only scanner at the Olin Neuropsychiatry Research Center. The pulse sequence was a single-shot spin echo EPI sequence (repetition time/echo time=6300/85msec, FOV=220mm, matrix 100, diffusion-sensitizing orientations=32, b=0 and 1000s/mm²) that covered the whole brain in 45 slices with 1.7×1.7×3.0 mm³ resolution. Three sequences were acquired for a total scanning lasting approximately 11 minutes. Visual inspection ensured that all DTI data were artifact-free (see Supplemental Materials for details). Diffusion-weighted images were distortion-corrected using gradient echo fieldmaps, then registered to a common non-diffusion-weighted image using a mutual information cost function as employed in FSL’s FLIRT toolbox(43 (link), 44 (link)) with eddy current corrections.(45 (link)) To avoid possible head movement-related signal contamination, any image with a scan-to-scan displacement >2 mm was discarded. The remaining images were concatenated and tensor calculated. A sample-specific mean FA image was calculated from all datasets, then tract-based spatial statistics (TBSS)(46 (link)) calculated the scalar FA measures for subject-specific skeletons. Data were spatially normalized to a common Montreal Neurological Institute (MNI) space template using FNIRT toolbox.(47 )

MRI scans were performed on a Siemens 3T Allegra head-only scanner. Two scans were acquired; 1) Sagittal T1-weighted magnetization prepared rapid acquisition gradient echo (MPRAGE) volumetric scans were acquired to serve as a guide in sulcal visualization during segmentation procedures in the same way an atlas is used as a visual reference (repetition time: 2,300ms, echo time: 2.93ms, slice thickness: 1 mm, 160 slices, in-plane voxel size 1.3×1.3mm, field of view (FOV) 256mm); 2) High-resolution oblique coronal T2-weighted fast-spin echo sequence scan (repetition time: 5,200 ms; echo time: 105 ms; slice thickness: 3mm; skip 0, 19 slices; in-plane voxel size: 0.39×0.39 mm. FOV: 200 mm).