Dhaka Univ. J. Sci. 59(1): 147-152, 2011 (January) A Proposed Interleaved Echo Planer Imaging Technique for High Resolution fMRI Md. Enamul Hoque Chowdhury 1 and Shahida Rafique Department of Applied Physics, Electronics and Communication Engineering, Dhaka University, Dhaka 1000, Bangladesh Email: enamul@univdhaka.edu , srafique@univdhaka.edu Received on 12. 11. 2008. Accepted for Publication on 25. 09. 2010 Abstract An interleaved Echo Planar Imaging (EPI) fMRI technique has been proposed here for obtaining spatially high resolution activation map overlaid on EPI image to reduce image acquisition time. First of all, the 2D and 3D anatomical high resolution and 3D + Time series (4D) low resolution functional images have been reconstructed and normalized. Slice timing correction for avoiding disorder and motion correction for small head motion during the scan has been provided using the post-processing image registration algorithms. The extent of translational and rotational head movements in fMRI data that can be corrected has also been determined and observed that 1-2 mm of translational and 2-4 0 (deg) of rotational head movement correction can be achieved. The effect of hemodynamic response (HDR) on the neural activation has been observed and the relevant activation map has been found for correlation coefficient, r > 0.20. In order to obtain highly reliable and noise-free activation map, spatial smoothing has been done using a Gaussian filter with different kernel width and 4 mm filter was found to be best with acceptable SNR. Frequency selective temporal filtering of fMRI data has been done to avoid cardiac, respiration and Cerebral Spinal Fluid (CSF) pulsation, which shows 0.10Hz upper cut-off frequency filtering is the most effective one. Finally high resolution functional and anatomical reference image have been obtained at 3.0T using the interleaved EPI technique. This fMRI analysis offers possibilities for improved neurological research and clinical neurosurgical applications. I. Introduction The ‘pictures of the mind’ that have been produced over the past few years have started to make a big impact on the way neuroscience is approached. It has been known that changes in blood flow and blood oxygenation in the brain (collectively known as hemodynamics) are closely linked to neural activity. When nerve cells are active they consume oxygen carried by hemoglobin in red blood cells from local capillaries. The local response to this oxygen utilization is an increase in blood flow to regions of increased neural activity, occurring after a delay of approximately 1-5 seconds. This hemodynamic response rises to a peak over 4- 5 seconds, before falling back to baseline (and typically undershooting slightly). This leads to local changes in the relative concentration of oxyhemoglobin and deoxyhemoglobin and changes in local cerebral blood volume in addition to a change in local cerebral blood flow. These differential signals can be detected using an appropriate MR pulse sequence as blood-oxygen-level dependent (BOLD) contrast. The ultimate goal of fMRI data analysis is to detect correlations between brain activation and the task the subject performs during the scan. The BOLD signature of activation is relatively weak; therefore, other sources of noise in the acquired data must be carefully controlled. This means that a series of processing steps must be performed on the acquired images before the actual statistical search for activation can begin [1]. In an fMRI experiment a subject is required to perform a task while his brain is being scanned by an MRI scanner. In order to achieve a high quality analysis, the fMRI slices should be aligned. Hence, the subject is requested to avoid head movements during the entire experiment. However, due to the long duration of such experiments, head motion is practically unavoidable. As a result, imaging time and image quality has traditionally been at odds for all manner of magnetic resonance imaging. Using Echo Planar Imaging (EPI) technique in fMRI, the temporal resolution can be increased 10,000 times in comparison to high resolution anatomical imaging techniques but causes the increment of noise and reduces spatial resolution of the image. The 2D Fourier imaging techniques (2DFT) suffer much less from susceptibility distortion than EPI does, and this is one reason why these techniques are used in routine clinical scans. It is not impossible to carry out fMRI using 2DFT methods, particularly the fast techniques such as FLASH, but EPI will always have the speed advantage over such techniques. This is because the entire image is acquired from single free induction decay (FID), whereas FLASH only acquires one line in k-space from each FID [2-4]. In this work, an attempt has been made to reduce image acquisition time while keeping almost similar high resolution in the anatomical imaging with high resolution activation mapping by proposing technique called interleaved EPI, a hybrid of EPI and 2DFT, for both functional and anatomical image acquisition. To increase spatial resolution in EPI, two or more separate k-space traversals (interleaves) have been used to acquire different sets of k-space lines that are combined to produce one large data set. Interleaved EPI offers real benefits in carrying out high resolution fMRI at high field.