[Mristudio-users] tractography in ex-vivo rat brain

[susumu]

First check the color map. If all are running along the same orientation, it
should have only one color (like all blue). Then there is something wrong.

The most common mistake is, forgot to turn off auto-scaling of the 7 images
in the scanner.

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Anitha Priya K
Sent: Wednesday, July 30, 2008 12:53 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] tractography in ex-vivo rat brain

Hi
We are trying to do tractography in an ex-vivo rat brain using DTI
Studio. The imaging parameters were:
    Gradient directions
    image 0 : [0,0,0]
    image 1 : [.707,.707,0]
    image 2 : [.707,0,.707]
    image 3 : [0,.707,.707]
    image 4 : [-.707,.707,0]
    image 5 : [.707,0,-.707]
    image 6 : [0,-.707,.707]
    diffusion weighting b = ~996
    image resolution: 128 *128*128
    voxel size: 0.164 * 0.117* 0.117 mm
    Coronal sections

The images are saved as unsigned int - 16 bit raw images. When we
analyzed the data with DTIStudio, all the fibers seem to be running
longitudinally (superior-inferior) and there are no fibers in the
transverse direction (radially).

Does your experience imaging rodent brains match these outcomes, and
if not could you provide us information on whether  additional or
specialized  processing is required when analyzing ex-vivo datasets
for rodents?

thanks
Anitha Priya Krishnan,  PhD graduate student in Biomedical Engineering
Walter O'Dell, PhD, Assistant Professor of Radiation Oncology, and
Biomedical Engineering
Delphine Davis, PhD, Assistant Professor of Imaging Sciences, and
Radiation Oncology
University of Rochester
Rochester, NY 14642
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