In-vivo Whole-Brain Volumetry from 7T MRI

MRI measurements were performed under 1–2% isoflurane anesthesia in a 70:30 nitrous oxide:oxygen mixture. Temperature was maintained through a circulating warm water system. Respiration rate was monitored during the measurements (Small Animal Instruments, Inc., Stony Brook, NY). T2-weighted images were acquired on a 7T MR scanner (PharmaScan 70/16 US; Bruker, Ettlingen, Germany) using a 20 mm quadrature volume resonator (Rapid Biomed). To cover the whole brain, a 2D T2-weighted RARE pulse sequence was used with 32 contiguous axial slices with 0.5 mm slice thickness and in-plane field of view of 25.6 × 25.6 mm. The imaging parameters were: matrix size 256 × 256, echo time spacing ΔTE = 12 ms, repetition time TR/effective echo time TE = 4,200/36 ms, bandwidth = 46,875 Hz, RARE factor 8, 4 averages, acquisition time 6:43 min.
The Allen brain atlas (Lein et al., 2007 (link)) was registered to individual MR images using the MATLAB toolbox ANTX (Koch et al., 2019 (link)) and the volume of each brain region was measured in mm³. For statistical comparison of brain region volume between groups a t-test (FDR, q < 0.1) was applied. Only regions with a size of >0.1mm³ (corresponding to 20 voxels) in at least one of the analyzed groups were included in the analysis. Both, absolute brain region volumes as well as brain region volumes normalized to whole brain volume were evaluated.