Monica K. Hurdal1,
Aaron Kline1,
Kelly Rehm2,
David Rottenberg2,3,
Stephen Strother4
1Department of Mathematics,
Florida State University, Tallahassee, FL, U.S.A. 32306-4510,
2Department of Radiology, University
of Minnesota, Minneapolis, MN, U.S.A. 55455,
3Department of Neurology, University
of Minnesota, Minneapolis, MN, U.S.A. 55455,
4Rotman Research Institute, Baycrest
Centre for Geriatric Care, Toronto, ONT, Canada M6A 2E1
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Objective:
Software which is readily available to the neuroscience community can be
used to reconstruct cortical surfaces from magnetic resonance imaging
(MRI) data. Topologically correct cortical surfaces representing a
white matter (WM) surface (which occurs at the white matter/gray matter
interface) and a gray matter (GM) surface (which occurs at the gray
matter/cerebrospinal fluid interface) can be created. Using these
surfaces, we present an approach for producing a cortical mantle volume
representing the gray matter. We then use this cortical mantle volume
to restrict the analysis of functional MRI (fMRI) data to the gray matter.
Methods: The
FreeSurfer software [1] is used to produce topologically correct WM and
GM surfaces from 16 subjects. By default, FreeSurfer translates a
surface so the center of the MRI volume is located at the origin. We
translate the surface back to "native" volume space so the surface
coordinates are located within the original (i.e. native) MRI
dimensions. The vertex locations of the triangles which compose the
surface are then converted to voxel locations in a manner that ensures
no voxel gaps, giving a voxel representation of the cortical surface. A
region growing routine is used to identify all voxels enclosed within
the WM surface voxel representation and also the GM surface voxel
representation. Any voxels inside this enclosed WM voxel region are
removed from the enclosed GM voxel region. The result is a voxel mask
that represents voxels which belong to the GM surface, voxels which
belong to the WM surface and voxels which belong in between the GM and
WM surfaces. We call this voxel mask the cortical mantle volume mask.
Results & Discussion: Figure 1 shows a cross-section of
the resulting cortical mantle volume imposed on an MRI slice. We are
using these masks to restrict fMRI analysis to
the cortical mantle. FSL [2] is being used to perform GLM analysis on a
block design parametric static force BOLD fMRI dataset [3] of the 16
subjects. The SPMs from two single runs for each subject are masked by
the cortical mantle mask. Correlation between the two SPMs generated
for each single run are computed using the unmasked SPMs and also using
the cortical mantle masked SPMs.
Conclusions: Construction
of a cortical mantle mask permits restricting analysis of fMRI data to
the cortical mantle. There have been a number of hypotheses regarding
the possibility of improved functional localization results using
cortical surfaces. This research represents an attempt at determining
whether fMRI analysis that is restricted to the cortical mantle plays a
significant role in these hypotheses.
References & Acknowledgements:
[1] Fischl, B. et al. Cortical surface-based analysis II: inflation,
flattening, and a surface-based coordinate system. NeuroImage 9:179-194,
1999.
[2] Smith, S. et al. Advances in functional and structural MR image
analysis and implementation as FSL. NeuroImage, 23:208-219, 2004.
[3] LaConte, S. et al. The evaluation of preprocessing choices in
single-subject BOLD fMRI using NPAIRS performance metrics. NeuroImage,
18:10-27, 2003.
This work is supported in part by NSF grant DMS-0101329 and NIH
grant P20 EB02013.
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