[Neuroimaging] Tractography normalization

[Ariel Rokem]

On Thu, Aug 13, 2015 at 9:40 AM, Jesus-Omar Ocegueda-Gonzalez <
jomaroceguedag at gmail.com> wrote:

> Nice examples!, thanks! =D
>
> The 'apparent' holes within the ROI maybe normal artifacts of the nearest
> neighbor interpolation (we are looking at just one slice, so I'm not sure
> if there are callosum labels in front and behind too). If it is an isolated
> hole within the warped ROI, and the original ROI had no holes, then I need
> to investigate what happened because the topology must not change.
> Unfortunately, I cannot run the full example because I don't have the
> 'tools' module.
>

One of those figures is a sum-projection through the volume. There really
is a hole in the ROI (I also looked at it in 3D).

The 'tools' module is a one-function file in that repository:

https://github.com/arokem/AFQ-notebooks/blob/master/tools.py



>
> On Thu, Aug 13, 2015 at 10:24 AM, Ariel Rokem <arokem at gmail.com> wrote:
>
>>
>> On Thu, Aug 13, 2015 at 8:06 AM, Jesus-Omar Ocegueda-Gonzalez <
>> jomaroceguedag at gmail.com> wrote:
>>
>>> Hi guys!, =)
>>> Ariel, in you example:
>>>
>>>>
>>>>> transform_streamlines(transform_streamlines(transform_streamlines(sl,
>>>>> affine), warp_field), np.linalg.inv(affine))
>>>>>
>>>>>
>>> in what coordinate system are the streamlines `sl` originally? are they
>>> in the subject's image (voxel units) or in the subject's physical space
>>> (mm. units)? I just would like to know what would be a typical use case for
>>> this.
>>>
>>
>> Streamlines are often saved in the subject's physical space (in mm). For
>> example, see these notebooks:
>>
>> https://github.com/arokem/AFQ-notebooks/blob/master/DTI-tracking.ipynb
>>
>> https://github.com/arokem/AFQ-notebooks/blob/master/AFQ-registration-callosum.ipynb
>>
>> Here, only a linear transform is applied to the streamlines, because we
>> are warping a callosum ROI into the subject's mean B0 space, but we might
>> want to go in the opposite direction as well, warping the streamlines to
>> the original ROI space.
>>
>> By the way - do you have any insight as to why the callosum ROI in the
>> latter notebook ends up with holes in it, when it is warped with the SyN
>> warp field?
>>
>>
>>
>>>
>>> --
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>>> -Proverbio chino.
>>> "We all are owners of what we keep silent and slaves of what we say"
>>> -Chinese proverb.
>>>
>>> http://www.cimat.mx/~omar
>>>
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>>>
>>
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>>
>
>
> --
> "Cada quien es dueño de lo que calla y esclavo de lo que dice"
> -Proverbio chino.
> "We all are owners of what we keep silent and slaves of what we say"
> -Chinese proverb.
>
> http://www.cimat.mx/~omar
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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