[Mrtrix-discussion] MRTrix Track visualization - fibernavigator

[Jean-Christophe Houde]

Hi all,

well, in fact, the current implementation of TCK loading in the Fibernav
relies on the q-form / s-form of the anatomy that is already loaded. When
something like this happens, it is most often caused because the last
anatomy that you loaded doesn't have the same affine transform (the s- or
q-form) as the one in the anatomy that was used to track your streamlines
in Mrtrix.

As Jan suggested, you could set the affine of your source anatomy to
identity before tracking, but that shouldn't be necessary. Instead, just
make sure that the last anatomy file you loaded is something that was in
the same space as your CSD (or any other model that you used for tracking).

Best,

--
Jean-Christophe


2015-06-18 5:29 GMT-04:00 Jan Schreiber <schreiber at cbs.mpg.de>:

> Hi Jean-Christophe,
>
> it's probably because the streamlines are in world-coordinates and as far
> as I know fibernavigator uses voxel coordinates.
>
> You might get a good result by replacing the transform (s- and q-form if
> you are using nifti format) with the identity transform before processing
> the data (be careful if your data is stored in radiologic convention!).
>
>
> Another solution might be to use BrainGL
> https://code.google.com/p/braingl/
>
> Hope that helps,
> Jan
>
>
>
> On 06/18/2015 10:11 AM, Hak Fujiyama wrote:
>
>> Dear Jean-Christophe,
>>
>> I have been searching for answers to my issue with the visualizations of
>> tracts created by MRTRIX. I came across your post on the
>> Mrtrix-discussion and thought that you may be kindly help me.
>>
>> I am trying to visualize tracts created by mrtrix with fibernavigator.
>>
>> But somehow our tracts doesn’t align with the individual T1 image
>> (please see attached “m1-m1tckWithT1FiberNav.JPG”), though it does in
>> Mrview (please see attached “m1-m1tckWithT1mrtrix.JPG”).
>>
>> I would appreciate if you could help me on this issue.
>>
>> Thank you for your help in advance.
>>
>> Best regards,
>>
>> Hak
>>
>>
>
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