We developed a simple technique for determining the three-dimensional trajectories of recording microelectrodes placed in the brain along the long axis of a recording chamber attached to the skull. The technique uses MRI, which has become readily available to most researchers who conduct electrophysiological experiments in non-human primates, but does not require long scans (a typical imaging session for us lasted 40 min), high-powered magnets (most of our imaging was done using a 1.5T scanner) or a stereotaxic apparatus. Briefly, a cylinder filled with a high-contrast agent (CuSO4-doped water) is placed snugly in the recording chamber and is imaged along with the brain. Multiple planes of section through the cylinder produce images of ellipses that are used to reconstruct the three-dimensional structure of the cylinder. This reconstructed cylinder can then be projected virtually through the image of the brain and compared to the locations of specific brain regions estimated from published atlases (see –) or known anatomical landmarks ().
This technique, which is intended to complement methods that use a stereotaxic reference frame to visualize anatomy and recording hardware (Miocinovic et al., 2007
), has given us two distinct advantages. First, it allows us to confirm whether or not the recording chamber, typically placed using stereotaxic methods during surgery, is positioned appropriately. Stereotaxic procedures define the location of any position in the brain relative to a known coordinate system (Horsely V, 1908
). Although stereotaxic procedures yield consistent results in smaller animals, neuroanatomical structures in larger mammals, such as macaques, are just roughly aligned with cranial landmarks (Glimcher et al., 2001
; Percheron and Lacourly, 1973
) and are subject to substantial inter-animal variability (Wagman et al., 1975
). Thus, this method is especially imprecise for monkey neurophysiology (Aggleton and Passingham, 1981
; Olzewski, 1952
; Percheron, 1975
; Percheron and Lacourly, 1973
; Saunders et al., 1990
; Subramanian, 2001
; Subramanian et al., 2005
) and requires verification and possible adjustment. Our method avoids the stereotaxic reference frame altogether and instead compares directly the location and orientation of the recording chamber and underlying brain structures.
Second, this technique allows us to determine where to place our microelectrodes within the recording chamber and how far to advance them in depth to target the brain area of interest. Although finding an appropriate recording site still requires a certain amount of searching, this technique has greatly reduced the amount of time needed to do so. Using this technique we have expeditiously located several regions of the cerebral cortex (MT, LIP, and FEF) and one brainstem structure (LC). In general, finding appropriate sites now takes us days instead of weeks of searching.
The precision of this technique depends on several factors. Our simulations show that the image processing algorithm is susceptible to errors produced by low SNR or spatial resolution of the MR images (). However, for reasonable values of SNR (>10) and resolution (0.7-mm isotropic voxels for a ~20-mm diameter cylinder) that we were able to obtain easily in our images, our image processing algorithm will provide >95% coverage of the recording chamber and an unbiased estimate of its long axis to within <1 mm up to ~2 mm in depth. This amount of error seems likely to be relatively small compared to other, less predictable sources of error that will influence the ability to use these images to target specific brain regions, including: 1) individual variability in the locations of specific brain regions relative to identifiable anatomical landmarks, particularly in larger animals like macaques (Wagman et al., 1975
); 2) movement of the brain relative to the skull (and recording apparatus); 3) variability in the day-to-day placement of microelectrodes within the recording chamber (a problem that can be minimized by using a fixed grid for guiding microelectrode placement, at the expense of spatial resolution), and 4) microelectrode trajectories that do not travel exactly parallel to the long axis of the recording chamber (because of flexible microelectrodes that can bend unpredictably when traveling through tissue, for example). These additional sources of variability make it difficult to envision fundamental improvements to the precision of this kind of MRI-based technique even if the SNR and spatial resolution were to improve substantially.
Our application is acute, extracellular recordings in the cerebral cortex of awake monkeys. The size of the monkey brain (~60–70 mm in length; (Martin and Bowden, 1996
) and our recording chambers (19 mm inner diameter) and the size (at least several mm across) and depth of the targeted brain regions (<~10 mm deep for cortical areas MT, LIP, and FEF; ~40 mm deep for LC; (Martin and Bowden, 1996
), Stanton et al., 1989
, Lewis and Van Essen, 2000
) all contribute to the appropriateness of this technique, which provides an estimate of microelectrode trajectories with a precision of <~1 mm. Smaller brains, recording chambers or targeted brain regions would all pose stronger challenges to this or any other technique that attempts to determine precisely the microelectrode trajectories that would intersect the chosen targets.