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K.E. Herold, W.E. Bentley, and J. Vossoughi (Eds.): SBEC 2010, IFMBE Proceedings 32, pp. 493495, 2010.

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A Simple Structural Magnetic Resonance Imaging (MRI) Method for 3D
Mapping between Head Skin Tattoos and Brain Landmarks
Mulugeta Semework
State University of New York, Downstate Medical Center, Brooklyn, USA
Abstract A successful brain surgery requires pre-surgery
localization of various brain areas. An accurate craniotomy,
which gives perfect access to such brain area of interest is
needed and is dependent on mathematically establishing the
relationship between head landmarks and structural magnetic
resonance image (MRI) scans. While typical stereotactic pro-
cedures rely upon external cranial landmarks and standard-
ized atlases for localization of subcortical neural regions, visu-
alization of the internal morphology of the brain in vivo can be
achieved by MRI. Our lab, when possible, also uses MRIs on
our post-surgical monkeys to get precise information on the
exact placement of implanted microwires. Our stereotactic
instrument and head-posts on the monkeys are compatible
with a magnetic resonance unit and we have developed a
model to analyze the magnetic resonance imaging results and
calculate 3D mappings between external landmarks, skin tat-
toos on the primates heads and brain areas of interest. This
allowed us to overcome the limitations, inaccuracies, and cost
prohibitions of the traditional stereotactic methods and helped
us make reliable localization of subcortical targets in the mon-
key brain.

Keywords Structural MRI, Structural MRI image analysis,
brain structure mapping, Stereotactic method, neurosurgery.
I. INTRODUCTION
With increased ease, power and accessibility of magnetic
resonance imaging (MRI), especially the high resolution of
T1-weighted structural MRI [1] there has been a growing
interest in using this technology to study brain structure,
function, development, and pathologies [2]. In what is now
a very common practice of implanting primates with micro-
electrode arrays (MEAs) for various research goals, there is
a common problem that arises from the inherent variability
of brain structures and skull anatomy between different
subjects. Since MRI is a non-invasive method that capital-
izes on the complex mosaic across the cortical sheet [3], it is
possible to solve much of this problem by taking individual
MRIs pre-surgery and be able to map structures of interest
and use established coordinates during the surgery. There is
variability between individuals in pattern of brain area fold-
ing, shape and size of cortical areas and relative locations
[3]. We and others observe individual differences in brain
anatomy even though the overall organization and relative
location with respect to each other stays the same. It is very
common to find errors in subjective guesses of location of a
brain structure just from skull topography alone. Moreover,
as standardized atlases are generally used for localization of
subcortical neural regions [4] a problem arises from such
poorly informed assumption of the location of underlying
brain structures and it is not uncommon to make a mis-
placed craniotomy. There is thus a need for a method to
make a reconstruction of the areas of interest and describing
the relationships within a reasonably acceptable mathemati-
cal error. This short paper discusses a recently developed
new method for expressing relationships between surface
markers, such as tattoos on head skin and underlying major
brain structures.
II. METHODS
A. MRI Procedure
Monkeys (Macaca radiata) are anesthetized in their
home cage with Ketamine (10-20 mg/kg) injection intra-
muscularly. We found that most of our monkeys remain
under for the duration of the scanning by just this drug
alone. For the MRI procedure, the anesthetized monkeys are
transported to the SUNY Downstate Medical Center (DMC,
also known as University Hospital of Brooklyn) Depart-
ment of Radiology. In the facility, after their head is stabi-
lized with earbars, the monkeys are placed into the scanner
chamber, and their heads fitted inside a 16-in. head coil.
Monkeys remain anesthetized during the MRI procedure, if
needed, with a supplemental injection of Ketamine. Since
the procedure takes only 30-50 minutes, the first anesthesia
injections are generally effective in maintaining stillness
inside the machine.
MRIs of brains are acquired on a Magnetom Symphony
Maestro Class Scanner, and the following parameters are
for a typical scan and can vary between monkeys and scans
(2). T1-weighted 3D MPRAGE MR images are acquired
through the entire brain using a TR = 1,500 ms and
494 M. Semework


IFMBE Proceedings Vol. 32

TE = 3.04 ms with no echo-train. Scan acquisition time will
approximately be 10 min. For each monkey the number of
signals were averaged to be three. Slices will be obtained as
0.5-mm thick contiguous sections with a matrix size of 256
256 and a field of view of 128 mm 128 mm, resulting in
a final voxel size of 0.5 mm 0.5 mm 0.5 mm.
After being transported back to their cages, monkeys
are allowed to completely recover from the effects of the
anesthesia.
All procedures are done per SUNY DMCs Animal re-
search regulations and the Joseph T. Francis lab protocols.
B. Code and User Interface
The image metadata from a DICOM file series is made
into a structure, a 3D array of the images is generated, and
previewed using a Matlab tool (5).
All of the analysis is done by a novel Matlab function
that imports the DICOM images and does the pre-
processing and detailed calculations. Currently, there is a
tested command line version of the code. The most recent
one is designed for a user with no Matlab programming
skills and is still being optimized. In short, it has a Graphic
User Interface (GUI) used as a front panel to make option
selections, such as importing slides, color maps, edging
methods, etc. that makes the analysis easy and user friendly
(Fig.1)



Fig. 1 Graphic User Interface for new MRI mapping method (a Canny
edged brain scan shown)

C. Image Processing
To help in the ease and perfection of the next procedures,
the scans are first enhanced, region of interest (ROI)
cropped, and then appropriately edged, a subjective process
that depends also on the quality of the scans and the result-
ing binary images. Depending on several factors, the
threshold for edging can be manually set.


Fig. 2 Sobel-edged and selected brain, skull and marker surfaces

As shown in Fig. 2 (which shows already highlighted
targets, in color), the edged scan is now ready to be point-
and-clicked, or, in case of the new code (GUI shown in Fig.
1), a ROI is first manually selected, and an automated track-
ing of this object throughout all the scans follows. There is
the option of deciding how many connected points to con-
sider in the analysis, colors to use, etc. in graphical display-
ing of the process.
D. Transformations
The user has the option of selecting skull or brain land-
marks to be used for this purpose. The outside markers we
use, skin tattoos, are identified in the MRI scans from vita-
min E tablets we affix to the skin during the scanning (yel-
low ellipses on Fig. 3).
A Simple Structural Magnetic Resonance Imaging (MRI) Method for 3D Mapping 495


IFMBE Proceedings Vol. 32

Once the outside and inside points are set, they are
tracked through all or few selected scans that are known to
contain them. The absolute distance between any two
markers (mDist) in the scans 3-D space is calculated as
follows:
) *th) | ) s - (s (| pw * ) | ) y - (y |
| ) x - (x | ( ( z} y, mDist{x,
2
2 1
2
2 1
2
2
1
+
+ =

Where x and y are the locations of the given markers (or
ROI and marker), th is scan thickness in mm and pw is
pixel width. Following this same convention, the new auto-
mated approach computes the normalized 2-D cross-
correlation of the target matrix template and the cropped
scan and finds the maximum coefficient and gives mDist in
same 3-D space.
III. RESULTS AND DISCUSSION
Out of the need to make a simple craniotomy that lands
on the brain structures that we are interested in implanting
multielectrode arrays, the above method was developed. It
is designed to map physical markers, tattoos on the mon-
keys heads, and the underlying major brain landmarks,
such as the central sulcus. As shown in Fig. 3 (left panel), a
pencil sketch on the skull of the predicted location of the
central sulcus (diagonal trace) corresponded well with the
actual finding after the craniotomy.



Fig. 3 Craniotomy sketch and matching central sulcus

As a proof of individual differences, we tried using the
coordinate system and marker distances that were generated
from one monkey on another one and the craniotomy was
off by at least half a centimeter. One challenge we faced
was the lower placement on the side of the face of some of

the skin landmarks which made it difficult to do sterile
procedures during surgery. These markers ended up hiding
deep in the stereotactic apparatus and therefore only two
locations had to be used, still with no error in location the
target.
IV. CONCLUSIONS
For the sole purpose of making a craniotomy above the
location of the brain structure we are interested in, we found
this method to be very useful and dependable. It eliminated
the need to widen craniotomies or make new ones to correct
errors. The current code refinement is expected to make this
method available for wide use and help improve structural
mapping success. A broader application of this method is
envisioned for structures that are hidden from view and
reach or are too topologically convoluted.
ACKNOWLEDGMENT
I thank everyone in the Joseph T. Francis lab at SUNY
DMC for their unreserved support in taking the MRI scans
and comments in developing this method. Westley Hayes,
thank you so much for your professional and speedy manu-
script editing.
REFERENCES
1. Saad Z, Glen D, Chen G, et al. (2009) A new method for improving
functional-to-structural MRI alignment using local Pearson correlation.
NeuroImage 44, 839848
2. Smith S., Jenkinson, M, Woolrich, M, et al. (2004) Advances in func-
tional and structural MR image analysis and implementation as FSL.
NeuroImage. 23 (2004) S208S219
3. van Essen, D, Drury, H, Joshi, S, and Miller, M (1998) Functional and
structural mapping of human cerebral cortex: Solutions are in the sur-
faces. Proc. Natl. Acad. Sci. USA. Vol. 95, pp. 788795
4. Saunders, R, Aigner, T & Frank, J (1990). Magnetic resonance imaging
of the rhesus monkey brain: use for stereotactic neurosurgery. Exp.
Brain Res. 81, 443446
5. Balkay, L (2005) DICOM Reader at
http://www.mathworks.com/matlabcentral/fileexchange/
7926-dicomdir-reader




Author: Mulugeta Semework
Institute: State University of New York, Downstate Medical Center
Street: 450 Clarkson Ave, box 31
City: Brooklyn
Country: USA
Email: mulugetas@gmail.com

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