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

Roan LaPlante rlaplant at nmr.mgh.harvard.edu
Sat Nov 21 15:13:50 EST 2015

By the way my program uses freesurfer binaries to do the coregistration
(and expects files organized in a freesurfer reconstruction). All of the
MR/CT methods use mutual information registration. There are python tools
that implement this type of algorithm but in my experience they were much
more difficult to work with. Freesurfer's mutual information registration
does some rather clever resampling which was much smarter than what I was
able to hack together in nipy.
On Nov 21, 2015 3:08 PM, "Roan LaPlante" <rlaplant at nmr.mgh.harvard.edu>

> 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
> best
> R
> 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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