[Mristudio-users] query regarding fibre tracking in rat brain

[krithika balasubramanian]

Dear Dr. Mori:
I am working on rat model of MS using Bruker 4.7 T animal MR scanner to
obtain rat brain images. For DTI I use the following parameters:
no of directions = 30, b values = 3 (0, 250, 855 s/mm2) (in addition to 5 A0
images), no. of slices = 7, slice thickness=  2 mm with no interslice gap.
 I recently started using DTI studio to carry out fibre tracking. I have few
queries related to fibre tracking for which i need clarification:

I am able to open my bruker raw data as philips 2dseq, and i had modified
the gradient table such that it consists of 95 directions ((30 dir x 3
b-values) + 5 A0 images). So i get a total of 95 images on which i carry out
tensor calculation and fiber tracking. However when i draw ROI after
clicking fibre tracking, it gives more of a colour coding within the ROI
instead of fibre tracts.
I tried opening the file in 3DMRI. In 3DMRI, the fibres are single coloured
and the colours need to be changed manually. Also, i do not get the brain
anatomical structure on which the fibres are visualized. Rather i get a
rectangular plane containing the fibres when i change the threshold value.
 In addition, i am unable to use the ROIeditor as i assume it does not
contain any atlas for rat brain. Also i am unable to use the Diifeomap.exe
(for 32 bit OS) that i downloaded from your website as it gives
error message that the file is corrupt (I use a 32-bit system).
So here are my questions:
1. Is there any atlas available for rat brain that can be used in ROI editor
and 3DMRI
2. How can i use the diffeomap?
3. How can we see the entire colour coded fibre tracts of rat brain (in the
RGB format indicating the Superior-inferior, right-left, up-down directions)
in 3DMRI/DTI studio
4. In fibre tracking, after increasing the tract-turning angle (say 70 deg)
 will the number of fibres (or colur codes) not decrease when compared with
lower angle (say 40 deg). But we observe more colour codes when the
tract-turning angle is increased. Can you kindly explain the reason for
this? Consequently, are the statistical details of fibres within an ROI in
DTI STUDIO correct and can they be reported?

Thanks in advance
Regards,

Krithika Balasubramanian
Ph.D student
Department of NMR & MRI facility,
All India Institute of Medical Sciences
Ansari Nagar
New Delhi 110029
India
email: krithika982 at gmail.com
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