Deep-learning (DL) is a new paradigm in the artificial intelligence field associated with learning structures able to connect directly numeric data with high-level patterns or categories. DL seems to be a suitable technique to deal with computationally challenging Brain Computer Interface (BCI) problems. Following DL strategy, a new modular and self-organized architecture to solve BCI problems is proposed. A pattern recognition system to translate the measured signals in order to establish categories representing thoughts, without previous pre-processing, is developed. To achieve an easy interpretability of the system internal functioning, a neuro-fuzzy module and a learning methodology are carried out. The whole learning process is based on machine learning. The architecture and the learning method are tested on a representative BCI application to detect and classify motor imagery thoughts. Data is gathered with a low-cost device. Results prove the efficiency and adaptability of the proposed DL architecture where the used classification module (S-dFasArt) exhibits a better behaviour compared with the usual classifiers. Additionally, it employs neuro-fuzzy modules which allow to offer results in a rules format. This improves the interpretability with respect to the black-box description. A DL architecture, going from the raw data to the labels, is proposed. The proposed architecture, based on Adaptive Resonance Theory (ART) and Fuzzy ART modules, performs data processing in a self-organized way. It follows the DL paradigm, but at the same time, it allows an interpretation of the operation stages. Therefore this approach could be called Transparent Deep Learning.