We describe a novel semi-automated pipeline which integrates advanced data analysis tools for MR and PET with advanced PET reconstruction correction methods (partial volume effect correction [PVC], motion correction [MC], attenuation correction [AC]) in a user-friendly Matlab graphical user interface (GUI). The reconstruction and analysis GUI is written in Matlab. Computationally intensive tasks in the pipeline are automatically transferred to a high-performance computing cluster and retrieved.

Descriptions of the commercial packages used can be found in their corresponding references. SPM8 [1] is used in MC and AC processing. Comkat [2] and PMOD [3] are used for kinetic modeling. FSL [4] and SPM8 are used for group analysis. Freesurfer [5] is used for regions-of-interest (ROI) definition and smoothing. Data preprocessing: Head-motion is derived from a number of sources: echo-planar MR images, MR-based motion navigators, and directly from the PET data when MR data is unavailable (eg during shimming). Subsequently, the ME-MPRAGE is reoriented to the reference position. Cortical and subcortical ROIs are labeled using FreeSurfer; similarly, the MPRAGE is registered to MNI-space for generating subjectspecific atlases.