Parkinson’s disease (PD) is characterized by neurodegeneration of the dopaminergic neurons in the substantia nigra pars compacta (SNc). MRI has been used to study neurodegeneration in the nigro-striatal system in the 6-hydroxydopamine (6-OHDA) rat model but with diffusion MRI1,2 or SPECT imaging1. Here we evaluated the nigro-striatal pathway degeneration using both diffusion and functional MRI We hypothesized that the neurotoxin would induce structural and functional alterations in the SN system.Fifteen Sprague Dawley male rats (300-450g) were stereotactically injected in the right striatum (STR) with 6-OHDA (N=10) or saline (sham condition) (N=5). Imaging was performed 3 weeks later (peak of the lesion3) at 11.7T (Bruker Biospec 117/16 USR horizontal bore, 750mT/m gradients, Paravision 5.1, Ettlingen, Germany) with a rat surface head coil for signal reception and a 72-mm resonator for signal emission. All animals were anesthetized with 1.5% Isoflurane. Local first and second order shimming was performed using a Bruker MAPSHIM macro based on a fieldmap acquisition (500μm isotropic resolution; first-TE=1.4ms; delta-TE=3.4ms). Anatomical T2-weighted (T2w) images were acquired with a multi-slice multi-echo (MSME) sequence; TR=8000ms; TE=13.5ms; Matrix (Mtx)=384x256; field-of-view (FOV)=3.84x2.56cm2; resolution(res)=100x100μm2; slice thickness=200μm; 128 slices; number of excitations (Nex)=1; acquisition time (Tacq)=34min. For resting-state fMRI, multi-slice echo-planar images (EPI) were acquired with TR=3000ms; TE=17.5ms; receiver bandwidth=400kHz; Mtx=96x96; FOV=3.84x3.84cm2; res=400x400μm2; slice thickness=400μm; 52 slices; 110 repetitions; 4 dummy scans to allow T1 steady-state; Tacq=5min30s. For diffusion imaging, a 3D EPI-based sequence was used with TR=300ms; TE=24.2ms; Mtx=128x96x96; FOV=3.2x2.4x2.4cm3; res=250μm isotropic; b-value=1500s/mm2; 81 directions; Tacq=42min. A fieldmap acquisition was used to correct EPI geometric distortions. Functional time-series were motion-corrected by rigid-body realigment to the first volume, spatially smoothed (gaussian kernel with FWHM=500μm) and corrected from physiological noise by using compCorr algorithm. DWI data were preprocessed with standard tools of fsl 5.07: eddy_cor for eddy curent corection and fugue for epi distortion correction with the field map acquisition. we then used dtifit to compute the tensor metrics. T2w brain template was created from the 11 individual images. To do so, for each rat, T2w was coregistered to the Karolinska rat brain template4 by using Ants software and averaged across the 11 rats. Diffusion and functional images were coregistered to our template by combining linear transformation of functional/diffusion images to the individual T2w and a non-linear transformation of the individual T2w to our T2 template. A total of six 6-OHDA rats and five sham rats were included in the data analysis (4 6-OHDA rats were excluded for misregistration issues). Regions of interest (ROI) were imported from the WHS rat brain atlas5, co-registered to our template and manually adjusted when necessary (e.g. to avoid the injection line) in both hemispheres in the STR, the SN, the internal capsule (IC), the globus pallidus (GP), the thalamus (TH), the motor cortex (M1M2), and the somatosensory cortex (S1S2). For each rat, and each pair of ROIs, functional connectivity (FC) was evaluated by Paerson correlation coefficient between the averaged functional time-series within each ROI. Finally, averaged Fractional Anisotropy were calculated within each ROI for each rat. Group differences between FC and FA measures were tested by using non-parametric Kruskall-Wallis rank test and considered significant if p<0.05.FA measurements showed significantly increase FA in the ipsilateral STR (p=0.03) and a trend for increased FA in the contralateral STR (p=0.07) in the 6-OHDA group compared to the sham group (Figure1). This increase is mainly due to the decrease of radial diffusivity and the relative preservation of axial diffusivity suggesting neuronal loss. In parallel, FC increases significantly between contralateral M1/2 and contralateral GP (p=0.02), between ipsilateral STR and ipsilateral GP (p=0.01) and between contralateral STR and ipsilateral GP (p=0.04) (Figure 2).This work showed significant alterations of functional connectivity and diffusion metrics in cerebral regions involved in the nigro-striatal system (STR, GP, TH, M1M2). Significant FA increase in STR, related to local neuronal loss, is associated with an increase of FC, suggesting a compensatory effect. These results will help improve our understanding of cerebral alterations and reorganization in PD pathology.As a perspective, we plan (i) to reconstruct the nigro-striatal pathway with diffusion-based tractography and to evaluate structural connectivity alterations; and (ii) to evaluate dopaminergic neuron depletion with histological markers and to correlate them with our MRI findings.