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Disease diagnosis with computer-aided methods has been extensively studied and applied in diagnosing and monitoring of several chronic diseases. Early detection and risk assessment of breast diseases based on clinical data is helpful for doctors to make early diagnosis and monitor the disease progression. The purpose of this study is to exploit the Convolutional Neural Network (CNN) in discriminating breast MRI scans into pathological and healthy. In this study, a fully automated and efficient deep features extraction algorithm that exploits the spatial information obtained from both T2W-TSE and STIR MRI sequences to discriminate between pathological and healthy breast MRI scans. The breast MRI scans are preprocessed prior to the feature extraction step to enhance and preserve the fine details of the breast MRI scans boundaries by using fractional integral entropy FIE algorithm, to reduce the effects of the intensity variations between MRI slices, and finally to separate the right and left breast regions by exploiting the symmetry information. The obtained features are classified using a long short-term memory (LSTM) neural network classifier. Subsequently, all extracted features significantly improves the performance of the LSTM network to precisely discriminate between pathological and healthy cases. The maximum achieved accuracy for classifying the collected dataset comprising 326 T2W-TSE images and 326 STIR images is 98.77%. The experimental results demonstrate that FIE enhancement method improve the performance of CNN in classifying breast MRI scans. The proposed model appears to be efficient and might represent a useful diagnostic tool in the evaluation of MRI breast scans.