[Neuroimaging] Dipy - Problem creating the fiber trackting of my data

[Eleftherios Garyfallidis]

Hi Jorge,

I am not sure what is the problem.

Do you calculate the tensors (fa, evecs) with Dipy too? Or loading them
from somewhere else?
I would suggest to do all the processing with Dipy if you can.

In the meantime can you share one of your datasets ? So, I can have a look ?

Best regards,
Eleftherios


On Tue, Jun 30, 2015 at 7:22 PM, Jorge Rudas <jrudascas at gmail.com> wrote:

> Hi again,
>
> I thought it would be more useful to give you more information about what
> we are trying to do:
>
>    - We have information of multiples subjects from 1.5T GE Health
>    Care resonator and 24 diffusion directions.
>
>    - This data have been converted from DICOM to .nii 4D by using dcm2nii
>    (the .bvec and .bval are generated automatically during the conversion).
>
>    - When in doubt of the quality of conversion, we reconstruct the model
>    tensor and tractography of the data after conversion, with MedINRIA and
>    tractography produced is very good.
>
>    - With DIPY, we basically tried to replicate the example *Deterministic
>    tracking with EuDX on Tensor Fields *(
>    http://nipy.org/dipy/examples_built/tracking_eudx_tensor.html#example-tracking-eudx-tensor)
>    using our data.
>
>    - For that purpose, we have only made a task of preprocessing
>    (segmentation of the brain using median_otsu of DIPY). We have no other
>    activity preprocessing.
>
>    - The rest of the implementation is exactly like the example.
>
> Regard
>
>
>
>
>
> Dear Dipy Team
>>>
>>
>>
>>> I have data from GE Medical Systems resonator, with 24 directions and
>>> only axial view.
>>>
>>> I using the examples for your documentation, specificaly
>>> http://nipy.org/dipy/examples_built/tracking_eudx_tensor.html#example-tracking-eudx-tensor
>>> .
>>>
>>> But, i get the fiber tracking bad. The data was convert using dcm2nii
>>> from DICOMs.
>>>
>>> Below, you find two link at my images of fiber tracking.
>>>
>>> https://www.dropbox.com/s/lc3wmv2yb1nz7uf/image%20%281%29.png?dl=0
>>>
>>
>>
>>> https://www.dropbox.com/s/gaguehp73qqgo0h/image%20%282%29.png?dl=0
>>>
>>
>>
>>>
>>> Any suggestions to improve the fiber tracking with my data?
>>>
>>> *Jorge Rudas*
>>> *National University of Colombia*
>>>
>>>
>>
>
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