[Mristudio-users] Fibertracking dorsal cingulum bundle

[mdfarid a r]

Thank you Dr Mori and Dr Hangyi,

Upon ur advice, I investigated the fibertracking and found that at all green
regions, fibertracking was in the superior-inferior direction while at the
blue regions, fibertracking was in the anterior-posterior direction. I have
swapped the y and z columns of the gradient table and now my fibertracks of
the cingulum have much better correspondence to the atlas.

The consequence also is that, I swapped the green and blue colour around. so
that my colormap and eigenvector map does not follow your book. I will try
proceeding in this way and see if I experience any other problems with
fibertracking.

Thanks also for directing me to the page about the "issue of +/- definition
of gradient tables". It helped me to understand the significance of the
eigenvector directions in x,y,z direction.

Regards,
Farid
On Wed, Jan 27, 2010 at 12:07 AM, susumu mori <susumu at mri.jhu.edu> wrote:

> 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
>>
>>
>
> _______________________________________________
> 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/20100127/6ba9b92f/attachment-0001.html