Diffuse degeneration of cortical and deep gray matter (DGM) structures is thought to play a major role in determining disease progression in multiple sclerosis (MS) [1,2]. The pathophysiological mechanisms leading to diffuse cortical and DGM degeneration in MS are still unknown. Histopathological investigations implicated neuroinflammation through microglia and/or macrophages activation in the pathogenesis of cortical and subcortical diffuse damage [3]. Activated microglia and macrophages upregulate the expression of the 18kDa translocator protein (TSPO), which can be detected in vivo by 11C-PBR28 positron emission tomography (PET) imaging [4]. Here, in a heterogenous MS cohort, we combined 11C-PBR28 imaging on a high resolution, integrated human MR-PET system with ultra high resolution 7 Tesla (7T) MRI to i) investigate the presence of activated microglia and macrophages throughout the cortex and DGM, ii) assess their relation with neurodegeneration, iii) and with measures of neurological disability (Expanded Disability Status Scale, EDSS) and information processing speed (Symbol Digit Modalities Test, SDMT) frequently affected in MS.Eighteen MS subjects (11 secondary progressive, SP, and 7 relapsing remitting, RR; mean±SD age=49±11 years; median, range EDSS=6.5, 2-7.5) and 12 age- and TSPO affinity binding (as assessed by the Ala147Thr TSPO polymorphism [5]) matched healthy controls (HC) underwent 90-minutes of 11C-PBR28 MR-PET (Siemens BrainPET). Anatomical 3T MR scans were simultaneously acquired for: a) cortical surface reconstruction, cortical thickness (CT) measurement, using FreeSurfer b) DGM segmentation (thalamus, hippocampus and basal ganglia), volume estimation, using FIRST-FSL c) MR-PET image registration (Figure1). Standardized uptake value (SUV) maps were created for 60-90-minute PET frame (1.25 mm isotropic voxels) and normalized (SUVR), to take into account global differences across subjects, to a pseudo-reference region with SUV levels similar in HC and MS. Seventeen patients underwent 7T (Siemens, 32-channel head coil) acquisitions of T2* gradient-echo sequences (0.33x0.33x1mm3) to segment intra-cortical (IC) and leukocortical (LC) lesions (Figure1). Five patients, however, were excluded due to motion artifacts, 4 patients had no cortical lesions (CL). Lesional, whole cortex and DGM masks were co-registered to 11C-PBR28 maps to extract SUVRs. In HC, SUVRs were obtained from cortex and DGM. Linear regression models were used to compare, in MS vs HC, SUVRs across GM (CL, whole cortex, DGM), as well as CT and DGM volumes, and to assess in MS the relationship between SUVRs, CT, DGM atrophy, and clinical metrics (EDSS, SDMT). Age, gender, TSPO affinity and intracranial volume were included as regressors when appropriate with a significant threshold of p<0.05 (we denote as p*, the p-value corrected for multiple comparisons and as p the uncorrected p-value). Using Freesurfer, a general linear model (GLM) was run on a vertex-by-vertex basis across the whole cortex (p*<0.05, corrected for multiple comparisons) to assess: i) differences in 11C-PBR28 SUVRs in MS vs HC ii) the relationship in MS between 11C-PBR28 SUVRs and clinical scores. Prior to GLM statistics, each individual SUVR map was coregistered to cortical surfaces, sampled at mid-cortical distance, smoothed along the surface with a 10 mm full-width at half maximum Gaussian kernel, and normalized to a common template surface. TSPO affinity and CT at the vertex level were used as nuisance factors.Relative to controls, MS subjects had increased 11C-PBR28 SUVRs in thalamus (~50%, p*=0.01), hippocampus (~40%, p*=0.002), basal ganglia (22%, p*=0.01). Increased 11C-PBR28 uptake was also observed in whole cortex (~18%, p*=0.01), and even more in CL (~36%, p*=0.01), with similar SUVRs between LCL and ICL (Figure2). Patients had decreased mean CT (MS=(2.3±0.1)mm, HC=(2.3±0.1) mm, p=0.05) and thalamic volume (MS=(8252±2280)mm3, HC=(9574±1284)mm3, p=0.006) than HC. Cortical thinning correlated with higher SUVRs in thalamus (p=0.02), hippocampus (p=0.03) and cortex (p=0.03). The cortical surface-based analysis disclosed a cluster of increased 11C-PBR28 uptake in MS vs HC in the middle temporal cortex of the right hemisphere, extending to the inferior temporal cortex (Figure3). Negative correlations were detected between SDMT scores and 11C-PBR28 uptake in the superior frontal and middle temporal cortex of both hemispheres,in the right transverse temporal and frontal cortex, and left lateral occipital and precentral cortex (Table 1, Figure3). Impaired SDMT scores were also associated with subcortical GM glial activationin thalamus (p=0.03) and hippocampus (p=0.02) Neurological disability (EDSS) correlated with increased11C-PBR28uptake in thalamus (p=0.02), basal ganglia (p=0.04), and whole cortex (p=0.05), though no regional cortical associations were found at the vertex-wise GLM analysis.Our data indicate that neuroinflammation in MS, likely mediated by activated microglia, is a diffuse process throughout cortex, particularly cortical lesions, and DGM and it is closely linked to neurodegeneration and poor clinical outcome.