This paper introduces image processing methods to automatically detect the 3D volume-of-interest (VOI) and 2D region-of-interest (ROI) for deep gray matter organs (thalamus, globus pallidus, putamen, and caudate nucleus) of patients with suspected iron deposition from MR dual echo images. Prior to the VOI and ROI detection, cerebrospinal fluid (CSF) region is segmented by a clustering algorithm. For the segmentation, we automatically determine the cluster centers with the mean shift algorithm that can quickly identify the modes of a distribution. After the identification of the modes, we employ the K-Harmonic means clustering algorithm to segment the volumetric MR data into CSF and non-CSF. Having the CSF mask and observing that the frontal lobe of the lateral ventricle has more consistent shape accross age and pathological abnormalities, we propose a shape-directed landmark detection algorithm to detect the VOI in a speedy manner. The proposed landmark detection algorithm utilizes a novel shape model of the front lobe of the lateral ventricle for the slices where thalamus, globus pallidus, putamen, and caudate nucleus are expected to appear. After this step, for each slice in the VOI, we use horizontal and vertical projections of the CSF map to detect the approximate locations of the relevant organs to define the ROI. We demonstrate the robustness of the proposed VOI and ROI localization algorithms to pathologies, including severe amounts of iron accumulation as well as white matter lesions, and anatomical variations. The proposed algorithms achieved very high detection accuracy, 100% in the VOI detection , over a large set of a challenging MR dataset.