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

Roan LaPlante rlaplant at nmr.mgh.harvard.edu
Sat Nov 21 15:08:44 EST 2015

Hi Chris,

I spent the better part of the last year writing a program in python that
does exactly this and tweaking the methods to work better.

Take a look at http://github.com/aestrivex/gselu

On Nov 21, 2015 2:51 PM, "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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