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

[Jorge Rudas]

Hi Eleftherios, thanks you for your answer.

I share you the raw data in this link:

https://www.dropbox.com/s/good87rel35ay8n/dicom.tar?dl=0

And, in this link you get the dicoms converted to nii 4D with dcm2nii:

https://www.dropbox.com/sh/acikf8r7j86ljnk/AACE5oYf9htbKLr370OcStTLa?dl=0

Additionally, attached to mail you can find the my implementation

Best regards,

*Jorge Rudas*





2015-06-30 18:43 GMT-05:00 Eleftherios Garyfallidis <garyfallidis at gmail.com>
:

> 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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>>
>>
>
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