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Overview of fMRI analysis

Oxford University Centre for Functional MRI of the Brain (FMRIB), John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK

View larger version (47K): [in a new window]   Figure 1. What are voxels? Shown here are surface renderings of 3D brain images. On the left is a high-resolution image, with small (1 mm x 1 mm x 1.5 mm) voxels; the voxels are too small to see. On the right is a low-resolution image of the same brain, with large (7 mm x 7 mm x 10 mm) voxels, clearly showing the voxels making up the image.

View larger version (20K): [in a new window]   Figure 2. An example time series at a strongly activated voxel from a visual stimulation experiment. Here the signal is significantly larger than the noise level. Periods of stimulation are alternated with periods of rest – a complete stimulation-rest cycle lasts 20 scans.

View larger version (15K): [in a new window]   Figure 3. Model waveform formation: the square waveform describes the input stimulation timing; the smoothed waveform results from convolving the first with the haemodynamic response function, a transformation which leaves the model looking much more like the measured data.

View larger version (25K): [in a new window]   Figure 4. Example design matrix with two explanatory variables; two different stimulations are being applied. Because they have different timings, they are modelled separately (Equation 2). Time is on the y axis, pointing downwards. Note that a column has two representations of the model's value at each point in time: the underlying intensity encodes the model's value at a particular time point, and so does the line graph.

View larger version (39K): [in a new window]   Figure 5. Example of modelling a non-linear interaction between stimuli. The first two EVs model the separate stimuli, whilst the third models the interaction, i.e. accounts for the "extra" response when both stimuli are applied together.

View larger version (13K): [in a new window]   Figure 6. (a) Rotation and (b) translation parameters estimated by a rigid-body motion correction procedure, as a function of scan number.

View larger version (25K): [in a new window]   Figure 7. Example slices from an example fMRI volume, (a) before and (b) after spatial filtering of 5 mm full width half maximum (FWHM).

View larger version (28K): [in a new window]   Figure 8. An example time-course from a single (activated) voxel. (a) Time-course before high-pass filtering. (b) After filtering, and plotted against the fitted model.

View larger version (39K): [in a new window]   Figure 9. The model, or design matrix, used in the general linear model analysis of the heat-warm experiment. EVs 1 and 5 model pain and warm, EVs 3 and 7 model conditioning to pain and warm, and the even numbered EVs are simply the temporal derivatives of the odd numbers; these allow phase shifts in the fitting.

View larger version (66K): [in a new window]   Figure 10. Various stages in the rendering of activation onto a high-resolution structural image.

View larger version (81K): [in a new window]   Figure 11. Comparison of (a) the standard space MNI 152 image and (b) the mean of the 18 subjects' high-resolution structural images after transformation into standard space. The mean of the subjects' MR "high-resolution" images is fairly blurred, due to the relatively low resolution of most of the structural scans taken for this study.

View larger version (36K): [in a new window]   Figure 12. Significant differences between the two subject groups in the pain-warm contrast.