Clinical two-dimensional (2D) MRI data has seen limited application in the early diagnosis of Parkinson's disease (PD) and multiple system atrophy (MSA) due to quality limitations, yet its diagnostic and therapeutic potential remains underexplored. This study presents a novel machine learning framework using reconstructed clinical images to accurately distinguish PD from MSA and identify disease-specific neuroimaging biomarkers. The structure constrained super-resolution network (SCSRN) algorithm was employed to reconstruct clinical 2D MRI data for 56 PD and 58 MSA patients. Features were derived from a functional template, and hierarchical SHAP-based feature selection improved model accuracy and interpretability. In the test set, the Extra Trees and logistic regression models based on the functional template demonstrated an improved accuracy rate of 95.65% and an AUC of 99%. The positive and negative impacts of various features predicting PD and MSA were clarified, with larger fourth ventricular and smaller brainstem volumes being most significant. The proposed framework provides new insights into the comprehensive utilization of clinical 2D MRI images to explore underlying neuroimaging biomarkers that can distinguish between PD and MSA, highlighting disease-specific alterations in brain morphology observed in these conditions.