[Neuroimaging] Tractography normalization

Ariel Rokem arokem at gmail.com
Thu Aug 13 17:24:19 CEST 2015


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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>
> http://www.cimat.mx/~omar
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