A computer-implemented method for generating information associated with an image of at least one region of a subject, comprising: receiving image data of at least one region within a brain stem of a subject acquired by at least one magnetic resonance scan that included a pre-pulse and a pulse sequence, wherein the pre-pulse has a flip angle between 150° and 425° and the pulse sequence is a gradient echo pulse sequence, wherein the at least one region within the brain stem contains neuromelanin, and wherein the pre-pulse is configured to saturate the at least one region; automatically segmenting the image data to determine voxels corresponding to neuronal tissue containing neuromelanin within the at least one region; processing the image data, wherein the processing includes analyzing the image data to determine at least quantitative information associated with the at least one region; wherein the quantitative information includes a number of voxels and contrast-to-noise ratio information; wherein the CNR information corresponds to an amount of neuromelanin in the region and the number of voxels corresponds to a number of neurons that contain neuromelanin; and outputting information associated with the at least one region, the information being based on at least the quantitative information; wherein the image data is magnetization transfer contrast image data acquired by a 3T MR imaging system, and wherein segmenting the image data to determine voxels corresponding to neuronal tissue containing neuromelanin comprises: disposing a number of target regions of interest corresponding to the region of interest; determining a signal intensity value for each voxel in each target region from the image data; determining a mean and a standard deviation of the signal intensity for each target region; determining a signal intensity difference for each voxel based on a comparison of the signal intensity value for each voxel to the mean and standard deviation in a corresponding target region; and generating, based on the signal intensity difference for each voxel, a binary map which indicates for each voxel whether or not it corresponds to neuronal tissue containing neuromelanin. receiving image data of at least one region within a brain stem of a subject acquired by at least one magnetic resonance scan that included a pre-pulse and a pulse sequence, wherein the pre-pulse has a flip angle between 150° and 425° and the pulse sequence is a gradient echo pulse sequence, wherein the at least one region within the brain stem contains neuromelanin, and wherein the pre-pulse is configured to saturate the at least one region; automatically segmenting the image data to determine voxels corresponding to neuronal tissue containing neuromelanin within the at least one region; processing the image data, wherein the processing includes analyzing the image data to determine at least quantitative information associated with the at least one region; wherein the quantitative information includes a number of voxels and contrast-to-noise ratio information; wherein the CNR information corresponds to an amount of neuromelanin in the region and the number of voxels corresponds to a number of neurons that contain neuromelanin; and outputting information associated with the at least one region, the information being based on at least the quantitative information; wherein the image data is magnetization transfer contrast image data acquired by a 3T MR imaging system, and wherein segmenting the image data to determine voxels corresponding to neuronal tissue containing neuromelanin comprises: disposing a number of target regions of interest corresponding to the region of interest; determining a signal intensity value for each voxel in each target region from the image data; determining a mean and a standard deviation of the signal intensity for each target region; determining a signal intensity difference for each voxel based on a comparison of the signal intensity value for each voxel to the mean and standard deviation in a corresponding target region; and generating, based on the signal intensity difference for each voxel, a binary map which indicates for each voxel whether or not it corresponds to neuronal tissue containing neuromelanin. disposing a number of target regions of interest corresponding to the region of interest; determining a signal intensity value for each voxel in each target region from the image data; determining a mean and a standard deviation of the signal intensity for each target region; determining a signal intensity difference for each voxel based on a comparison of the signal intensity value for each voxel to the mean and standard deviation in a corresponding target region; and generating, based on the signal intensity difference for each voxel, a binary map which indicates for each voxel whether or not it corresponds to neuronal tissue containing neuromelanin.