[Neuroimaging] Co-registering MRs to CT in python?

[Ariel Rokem]

Hi Chris,

I don't know that they've been used for this purpose before, but you might
want to try some of the tools for registration that are in dipy:

http://nipy.org/dipy/examples_built/syn_registration_3d.html#example-syn-registration-3d


Cheers,

Ariel


On Sat, Nov 21, 2015 at 11:50 AM, Chris Holdgraf <choldgraf at berkeley.edu>
wrote:

> Hey all - I'm in an electrocorticography lab that's trying to update the
> process we use for localizing electrodes on a patient's brain. Right now we
> get a pre-operative MRI, as well as a CT scan after electrodes have been
> implanted. In order to localize electrodes, we need to co-register the CT
> to the MRI and then define electrode locations on the CT.
>
> Right now, all the tools I've seen for this are in Matlab. They generally
> use either Fieldtrip (e.g., this
> <http://www.fieldtriptoolbox.org/faq/how_can_i_place_electrodes_on_an_anatomical_ct_or_mr>)
> or some custom code that uses SPM / FSL under the hood.
>
> I am wondering if tools like this exist in python as well, or if we're
> restricted to using Matlab. Obviously some steps in the pipeline might be
> missing (e.g., selecting electrodes in a CT scan and applying a label to
> them), but if the other steps are there (e.g., co-registering a CT to an
> MRI etc) then I may try to spend time filling in the missing holes.
>
> Anyone know of good resources along these lines? I've been playing around
> with nibabel for I/O and pysurface for doing surface recons of our MRIs,
> but haven't found a good tool for co-registration etc.
>
> Any info is appreciated (and apologies if this is a naive question).
>
> Chris
>
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