[Mristudio-users] Fibertracking dorsal cingulum bundle

[susumu mori]

Farid,

There are several points I want to make, although at this point, I'm not
100% sure what went wrong;

> First of all, your tracking results do look odd.
> Second, I'm concerned about the non-conventional orientation of your
image. The upper right must be axial and the lower right has to be the
coronal. Also, your sagittal is 90 degree rotated.  In DtiStudio, the X axis
(horizontal) of the upper right and the lower right images are the
anatomical right-left, which is assigned red. This part is correct. Then the
Y (vertical) of the upper right image and the X axis (horizontal) of the
lower left image is the anatomical anterior-posterior, which is assigned
green. In your image, these axes have blue color and anatomical
superior-inferior. In other words, the definition of the green and blue
(anterior-posterior and superior-inferior) are switched. I'm not sure how it
happened. If you used our software for image normalization, the consistency
of the orientation definition (which is always the Radiology convention) is
guaranteed, but if you used another software at some point, it's hard for us
to track down the problem.
>There is always the issue of +/- definition of gradient tables. Please
refer description at "
https://www.mristudio.org/wiki/user_manual/DTI_Studio_User_Manual/fiber_tracking"
that explains the issue. Before you apply any image transformation, you have
to make sure that this +/- issue is correctly addressed. Practically, you
need to confirm that you can get correct fiber tracking BEFORE you do any
transformation (normalization) of a data; you want to make sure tracking is
right in the native space.
> Another issue is that you need to transform (normalize) the tensor to
create a good population-averaged DTI data. The tensor transformation
requires special algorithm for tensor reorientation.

MriStudio offers DiffeoMap (formerly known as Landmarker) that provides the
state-of-the-art tensor normalization tools (
https://www.mristudio.org/wiki/user_manual/landmarker). In this way, you
don't have to worry much of the issues described above.

On Mon, Jan 25, 2010 at 7:38 PM, mdfarid a r <faridisme at gmail.com> wrote:

> Dear DTIStudio users,
>
> I am interested in investigating the cingulum bundle but am having trouble
> fibertracking the cingulum bundle.
>
> Based on the ColorMap0 and Eigenvector0 values in the region of the dorsal
> cingulum bundle, I would expect fibertracking to occur in an
> anterior-posterior manner but it is not the case.
>
> 1-ColorMap0.jpeg shows the ColorMap0. At the cingulum bundle region, the
> 2nd value is the greatest among the 3. (eg: 19,126,27 or 6,136,40)
>
> 2-Evector0.jpeg shows the Eigenvector0. At the cingulum bundle region, the
> 2nd value is the greatest among the 3. (eg: -0.21,0.95,-0.20)
>
> 3-fibertrack.jpeg is obtained by fibertracking using the binary image of
> the left cingulum mask from WMPMII
> The threshold criteria is restrictive so that not too many fibers obstruct
> the visualisation of the cingulum (threshold criteria is 0.3 for minimum FA
> and angle of 50degrees). The resulting fibertrack is still unexpected
> because it does not traverse in anterior-posterior manner but in the
> dorsal-ventral manner.
>
> Fibertracking at 0.15 minimum FA and angle of 70degrees. results in
> 4-fibertrack.jpeg. I further select the cingulum bundles by using the ROI
> AND operation at different coronal slices.
>
> At coronal slice 101, I am still able to obtain reasonable fibertrack
> results. 5-fibertrack.jpeg, the fibertracks lie in the cingulum region that
> is expected and extends over around14-18 slices from 101 to 114.
>
> However, as I try to delineate the cingulum bundle at more anterior coronal
> slices the cingulum is more horizontal, the fibertracking result
> delineates in dorsal-ventral manner. In the 6-fibertrack.jpeg, the
> fibertracks obtained extend over only 7 slices.
>
> I do not understand how this is so because the ColorMap0 and the
> Eigenvector0 seem to indicate that the principle diffusion direction is
> indeed in the anterior-posterior direction.
>
> -----------
> Some other information
> The image I used is a group registered to the JHU-MNI atlas. The images are
> averaged across many subjects to increase signal to noise ratio. However,
> when i repeat fibertracking on single subjects, the fibertracking results
> are still more dorsal-ventral than anterior-posterior.
> ------------
>
> Pls offer any suggestions. I really need the help. I can offer more
> additional information on my problem if required.
>
> Thank you in advance. I would really appreciate it.
> Regards,
> Farid
>
> _______________________________________________
> Mristudio-users mailing list
> Mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> Mristudio-users-unsubscribe at mristudio.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100126/79a4125d/attachment.html