Neuroimaging Assessment of Subarachnoid Hemorrhage - Animal Models of Acute Neurological Injuries: Injury and Mechanistic Assessments - page 431

4. Notes
1. Detailed protocols for the induction and description of SAH
models are described in Chaps. 26 - 27 of this topic. Prior to
adoption of a model or attempting new research into SAH one
should always consult with a veterinarian to obtain guidance as
institutional rules and directives may vary.
2. Scheduling experiments and animal surgery may in some labo-
ratories require coordination with user facilities that provide
access to these imaging instruments. Some of the user facilities
may also charge a fee for imaging. It is recommended that the
user meet with the imaging facility manager to discuss the tim-
ing, experimental design, and associated operational issues
related to noninvasive imaging. It should also be noted that
while in vivo imaging is optimal, ex vivo imaging after tissue
fi xation can also provide valuable data.
3. The described protocol will use SPIN to elucidate the basic
mechanisms underlying SWI image processing. Others have
reported programming within program environments, such as
Matlab and IDL. It should be noted that some preprocessing
of the images may be required, such as noise reduction algo-
rithms, skull stripping routines, and other user-dependent
issues. Volumetric reconstruction of the SAH lesion can also
be accomplished using commercially available 3D reconstruc-
tion software programs, such as Amira. However, free software,
such as NIH image, can also be used to extract and visualize
imaging datasets. Often however, these free programs are not
as powerful and 3D reconstruction may not optimal.
4. Other MR sequences can be utilized depending on the research
questions. Sequences, such as diffusion-weighted, T2-weighted,
and T1-weighted imaging, can be useful within the appropri-
ate research context.
5. It is always recommended that the users optimize their system
settings prior to embarking on a full research program. MR
system performance can vary widely and is often dependent
upon the hardware in use. Use of different coils can also
improve signal-to-noise ratios and choice of coil may signifi -
cantly impact the desired results. Finally, use of alternate imag-
ing parameters or coils during the experimental period can
alter the imaging datasets and may make it diffi cult to compare
datasets.
6. The phase images must be fi ltered to remove the phase aliasing
artifacts that look like zebra stripes across the image. This is
done with a high pass fi lter. The fi lter size must be selected