[Mristudio-users] Fibertracking dorsal cingulum bundle

Wed Jan 27 08:20:33 EST 2010

It seems that you got the matching between the vector orientations and
anatomy right. What is not still right (well it is not right or wrong. It's
just a convention) is that usually, the first dimension of the data (the x
element of your 3D data) is assigned red, second (y) green, and third (z)
blue, which usually coincide to right-left, anterior-posterior, and
superior-inferior. In your case, the order of the data matrix is right-left
/ superior-inferior / anterior-posterior. It's just the matter of the order
of your 3D matrix.

On Wed, Jan 27, 2010 at 5:21 AM, mdfarid a r <faridisme at gmail.com> wrote:

>
> 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
>>>
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>>
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