[Neuroimaging] Tractography normalization

[Jesus-Omar Ocegueda-Gonzalez]

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.


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?
>
>
>
>>
>> --
>> "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
>>
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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
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