Functional MRI

Data acquisition in functional MRI

Denis Hoa

To cope with the constraints of temporal resolution and T2* sensitivity, functional MRI sequences are generally of the ultrafast echo planar type (GE-EPI), with small matrixes (and thus weaker spatial resolution). The BOLD contrast obtained is very poor (low percentage of signal variation). Acquisitions need to be repeated in time, for different activation tasks, in order to conduct a statistically correlated comparative study of the signal variations measured in each pixel and variations in task. Differences in activation will thus relate to the difference between the two tasks.


The task sequence and mode of repetition constitute the activation paradigm. It consists of at least one reference task, and another task whose only difference is in the activity we wish to study (figures 14.2 and 14.3).


For instance, for motor activities, rest could be the reference activity, and repeated finger movements, the activity. For cognitive activities (language, interpretation, memory...), the protocols are more complex and the design of relevant tasks more subtle. It is also possible to simultaneously record data on patient responses during the examination (frequency of movements, stimulus-response time, correct or incorrect response...) to be integrated into the statistical analysis model.


Experimental paradigms in functional MRI

  • Block design: the activities are organized into blocks of several seconds’ duration, alternating at regular intervals. Within the same block, the hemodynamic responses will overlap and accumulate before reaching a plateau.
  • Event-related design: activities or stimuli that are either single or presented in short repetition, in a sequence that may be pseudo-random (to avoid the phenomenon of anticipation), possibly including measurement of response performance (response delay and accuracy…). The local hemodynamic response is thus evaluated for the different activities.

The theoretical curves of the hemodynamic response and the BOLD signal are established according to the type of design chosen and the time course of the sequence of conditions or tasks. They namely take account of the interval between neuronal activation and the measured hemodynamic response. In the case of rapidly repeated tasks, the sum of their effects results in a hemodynamic plateau response. This model forms the basis for statistical analysis, focused on pixels whose signal changes are linked to the paradigm.


The limitations and disadvantages of BOLD contrast functional MRI are linked to:

  • the distance between activated neurons and vascular variation in the oxyHb/deoxyHb ratio, leading to imprecisions in locating the activation zone
  • movement artifacts (movements of the head, vascular pulsations, breathing…) and magnetic susceptibility (signal distortion and loss at interfaces with the bones, the air, hematoma or at post-operational stage).

As in MRA, diffusion and perfusion MRI, parallel acquisition techniques will increase temporal resolution and reduce the artifacts in echo planar sequences by reducing echo time.


Functional MRI by spin labeling


This functional MRI technique consists in applying the spin labeling method used in perfusion MRI to detect variations in perfusion after brain activation.
This alternative to functional MRI by BOLD contrast is effective (more sensitive and less variable) for tasks repeated at low frequency. However less volume is explored in spin labeling.