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

[Chris Holdgraf]

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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