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Background  Because computers are used in many aspects of today’s life, it seems necessary to include them in teaching and assessment processes.    Method  The aims of this cross-sectional study were to construct a multidimensional valid scale, to identify the factors that influenced the nature of student motivation on Computer Based Testing (CBT), to recognize how students self-regulated their activities around CBT, and to describe the efficiency of autonomous versus controlled situations on motivation. The study was carried out among 246 Iranian Paramedical Students of Tabriz Medical Sciences University, Tabriz, Iran; 2013–2014.  The researchers prepared a questionnaire, based on the Self-Determination Theory (SDT), containing 26 items with a five-point Likert scale. It was prepared according to a previous valid questionnaire and by sharing opinions with some students and five professors. The factor analysis was done to perform instructional and exploratory factor analysis.    Results  The Kaiser-Meyer-Olkin(KMO) measure was performed and variables were correlated highly enough to provide a reasonable basis for factor analysis. The selected 4 factors determined a 60.28% of the variance; autonomy 26.37%, stimulation 14.11%, relatedness10.71%, and competency 9.10%.    Conclusion  A questionnaire was prepared and validated, based on SDT variables. The results indicated that autonomous extrinsic motivation correlated positively with intrinsic motivation and CBT. There was a general positive attitude towards computer-based testing among students. As students became intrinsically motivated through the promotion of autonomous regulation, CBT was recommended as a proper test mode.    Electronic supplementary material  The online version of this article (10.1186/s12909-018-1249-4) contains supplementary material, which is available to authorized users.

Conversion of extrinsic into intrinsic motivation and computer based testing (CBT)