Functional magnetic resonance imaging (fMRI) performed by echo-planar imaging (EPI) is often highly distorted, and it is therefore necessary to coregister the functional to undistorted anatomical images, especially for clinical applications. This pilot study provides an evaluation of human and automatic coregistration results in the human motor cortex of normal and pathological brains. Ten healthy right-handed subjects and ten right-handed patients performed simple right hand movements during fMRI. A reference point chosen at a characteristic anatomical location within the fMRI sensorimotor activations was transferred to the high resolution anatomical MRI images by three human fMRI experts and by three automatic coregistration programs. The 3D distance between the median localizations of experts and programs was calculated and compared between patients and healthy subjects. Results show that fMRI localization on anatomical images was better with the experts than software in 70% of the cases and that software performance was worse for patients than healthy subjects (unpaired t-test: P = 0.040). With 45.6 mm the maximum disagreement between experts and software was quite large. The inter-rater consistency was better for the fMRI experts compared to the coregistration programs (ANOVA: P = 0.003). We conclude that results of automatic coregistration should be evaluated carefully, especially in case of clinical application

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