AnalyzeDirect Karla J. Suchacki et al. The serotonin transporter sustains human brown adipose tissue thermogenesis Nature Metabolism.
Publication Date
August 3, 2023
How Analyze was Used
“PET–MR scanning protocol and analysis:
All participants received 75 MBq of 18F-FDG 1 h before being placed supine on a Siemens mMR scanner (Siemens Healthineers). Following initial localization, a standard MRAC_GRAPPA scan was acquired for each bed position, used to calculate a standard umap for attenuation correction. A three-dimensional T1-weighted Dixon VIBE acquisition was used to generate images at 1.34 and 2.56 ms (repetition time (TR) = 4.02) to calculate a fat fraction map (FFM) as outlined below. 18F-FDG uptake by BAT was quantified using Analyze v.12.0 (AnalyzeDirect). We developed a semi-automated process to standardize the PET/MRI analyses. Following registration, the MRI fat and water images were used to generate a FFM of each participant using the following equation:
Fatfraction(%)=(Signalintensities(SI)fat/(SIfat+SIwater))×100
A median spatial filter was applied to the FFM, and any voxels below 50% fat fraction (that is not adipose tissue) were removed to generate a fat fraction region of interest (ROI). The registered PET images were loaded and thresholded using the BARCIST criteria (a standard uptake value (SUV)lean of ≥1.2 g ml−1 for each participant9). Any remaining ROIs that encompassed the brain were manually removed. Voxels meeting both the FFM and PET thresholds were analysed. Cervical, supraclavicular and axillary depots were tagged together (classified as supraclavicular or SCV for simplicity), whereas paraspinal BAT was tagged separately. Finally, image erosion with a (3 × 3 × 1) structuring element was applied to the BAT ROIs to remove PET blooming and boundary artefacts. The effect of sertraline on 18F-FDG uptake by BAT was similar irrespective of whether image erosion was performed (see Source data for Fig. 3 and Extended Data Fig. 4). Data are presented for the BAT SUVmean and BAT volume, in addition to total 18F-FDG uptake by BAT (SUVmean multiplied by BAT volume) as previously described20.
For skeletal muscle analysis, ROIs from the pectoralis major, psoas major, sternocleidomastoid, longus colli and trapezius muscles, and in abdominal subcutaneous adipose tissue, were drawn manually using the MR water image, ensuring ROIs were identically sized and positioned at both study visits. These ROIs were applied to the registered and filtered PET images as described above for analysis.”
Keywords
Fat metabolism, Obesity, Transcriptomics, Brown adipose tissue, BAT, Brown fat
Author Affiliation(s)
University of Edinburgh, Edinburgh, United Kingdom
