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

[Eleftherios Garyfallidis]

Hi Jorge,

Found the problem! :)

The problem you had was that your datasets did not have isotropic voxel
size. Your voxel size was (0.9375, 0.9375, 5.0).
Tracking is not recommended when you have such difference in the voxel
sizes across the different slices. That is why
we don't support tracking in EuDX from non-isotropic voxel sizes.

But anyway you can still use these datasets if you use the reslice function
from Dipy. Then you can  reslice your datasets
to have isotropic size. I went to (2.0, 2.0, 2.0) for example.

Have a look in your updated script in the attachment.

Happy hacking!

Best regards,
Eleftherios


On Tue, Jun 30, 2015 at 10:56 PM, Jorge Rudas <jrudascas at gmail.com> wrote:

> 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*
>>>>>
>>>>>
>>>>
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>>
>>
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>
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