1. University of Illinois at Chicago
Laboratory for Product and Process Design
East Campus Room 4052
Director: Dr. Andreas Linninger
August 13, 2013

2.  The aim of this study is to compare the cerebrospinal fluid spaces
of the normal rabbit and hydrocephalus model and to compare
the volume changes using image reconstruction software
applications.
 This study employed both manual and automated segmentation
methods, in-vivo and ex-vivo to perform 3-D reconstruction of
the ventricular system.
 The goal of the study is to reveal the normal and hydrocephalus
SAS using these software applications and use these findings to
improve the treatment of hydrocephalus.
 Imaging modalities, 3-D angiography and MRI, in conjunction with
image reconstruction contribute to the analysis of hydrocephalus
research. There are challenges still to be tackled for the tissue
preparation and image acquisition of small animal ex-vivo MRI.
 ImageJ and MIMICS are powerful image processing tools which
can be used to analyze and understanding how the brain responds
to a hydrocephalus state.
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3. GOALS RELEVANCE OF OUR RESEARCH
1. To measure the volume of
the ventricular system of a
normal rabbit between a
hydrocephalus model
2. To create 3-D Medical Image
reconstruction of the rabbit’s
subarachnoid spaces and central
nervous system
3. To generate the basic
technical and experimental
procedures of the MRI for small
animals ex-vivo
 To utilize the volume mesh as
a mean to qualify the
differences of the normal
rabbit with a hydrocephalus
model.
 To perform ex vivo on brain
slice preparations
 To get a better brain image
 To understand the issues and
challenges related to small
animal MRI experiment
including design, data
acquisition, and processing.
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4. Imaging Reconstruction Flow Chart
Medical
Images
Segmentation
Masks
3 D Object
Surface MeshVolume Mesh
Computational
Dynamic Flow
Simulation
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5. Figure 1: MRI image showing an axial
slice of the rat CNS 5
Figure 2: MRI image showing an axial slice of the rat CNS
with the segmentation masks corresponding to CSF space
(pink) and CNS tissue regions (blue)
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The parameters used for obtaining the MRI images on a 9.4T animal MR scanner (Agilent) were as
indicated: Tr =2800ms, Te =16.38ms, averages =2, matrix =256x256, slices =15, Thickness
=0.195mm, gap =0mm, orientation: axial

6. Figure 3: Screenshot of the 3D of the
CSF space of the rat
Figure 4: MRI image showing an axial slice of the rat
CNS with the segmentation masks corresponding to CSF
space (pink) and CNS tissue regions (blue)
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Mask A
Mid spine to the end of the
spinal canal region
Mask B
Upper brain to mid spine region

7. 7
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Figure 5 Figure 6

8. 8
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9. 9
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Figure 8: Subtracted surface mesh obtained by Boolean subtraction of meshes
corresponding to CNS space and CNS tissue.
CNS SAS
=
CNS
tissue
Central Nervous
System

10. Definition
Figure 9: Brain ex-vivo and a
photograph of a brain coronal plane.
Magnetic resonance imaging
(MRI)
A technique whereby the
interior of the tissue can
be accurately imaged;
involves the interaction
between radio waves and
a strong magnetic field.
MR Microscopy can resolve
volumes of down to 50
mm³ (clinical MR does
1mm³) use for small
animal experiments (in
place of destructive
histology)
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11. An angiography image
of the experimental
set-up.
Dr. Basati induced hydrocephalus
with a butterfly needle
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12. 12
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Brain Model Results of the
hydrocephalus rabbit
Image Reconstruction in
rat’s
CNS
Hydrocephalus has not
produced in rabbits.
Digital Subtraction
Angiography
Next steps:
To understand the issues and
Challenges related to small
MRI experiment including
design, data acquisition and
processing.

13.  8/7/2013-Next Steps
To utilize the volume measurement as a mean to qualify
the differences of the normal rabbit with a
hydrocephalus model.
To observe an underlying hydrocephalic rabbit ‘s soft-tissue
brain model
To understand the issues and challenges related to small
animal MRI experiment including design, data
acquisition, and processing.
To understand what is 3-D rotational angiography
To generate my final report, video and poster
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14.  Abstract ID: 9970 Title: Small Animal Magnetic Resonance Imaging: Current Trends, Challenges and
Perspectives for Pathological Imaging.
 Benveniste H. Blackband S. 2002. MR microscopy and high resolution small animal MRI:
Applications in neuroscience research. Prog Neurobiol 67: 393-420.
 Budinger, T.F. Lauterbur, P.C., 1984. Nuclear magnetic resonance technology for medical studies.
Science 226, 288-298.
 D’Arceuil H. Liu, C., Levitt, P. Thompson, B., Kosofsky, Crespigny, A. 2007. Three-dimensional high-
resolution diffusion tensor imaging and tractography of the developing rabbit brain. Dev Neurosci
30, 262-275
 Driehuy B., Nouls J., Badea A., Bucholz, E., Ghaghada K., Petiet A., and Laurence W. Hedlund L.
W. 2008. Small animal imaging with magnetic resonance microscopy. Volume 49, 1. 35-53
 MRI Physics 1: Image Acquisition
 Description: Increases signal/noise: antenna ... Felix Block and Edward Purcell ... Purcell. 6. How fast do hydrogen atoms
spin? Field Strength (Tesla) 180. 40. 1.0. 4.0 ... – PowerPoint PPT presentation
 http://www.loni.ucla.edu/MAP
 This website provides information on digital web based mouse brain atlases that are based on
MR microscopy data.
 http://mouseatlas.caltech.edu/13.5 pc/
 This website provide another mouse brain atlas.
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