Rich,

You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for matlab, and freesurfer.

First run recon-all on the patients T1 (after acpc aligning in Spm). Then take the resultant orig.mgz file (convert to .nii using mri_convert orig.mgz orig.nii), and corregister the post-op CT to it using SPM's normalized mutual info. routine. To do this: 1.) open matlab, 2.)type spm at the prompt, 3.) chose fMRI from the gui pop up, 4.) pick corregister (est. and write) from the top left of the spm gui. Then chose the Orig.nii as the reference image, and the patients pos-op CT as the target.

Open the corregisterd CT (rCT.nii), the Orig.nii, and pial surface in freeview. Click on each electrode in the CT, and copy the xyz coords from the bottom left into a text file or matlab matrix (it will list the surface RAS coords in bottem left of freeview, which is what you want to display on the freesurfer pial surface). 

Let me know when you get that far and I'll send you a link to some code that will help you visualize the pial surface with overlaid electrodes.

-zack

On Wed, Oct 29, 2014 at 7:28 PM, rwlodar2@uic.edu <rwlodar2@uic.edu> wrote:
I have some post-op CT's for some of my patients but not all, do you have
a link or could you explain how to coregister so I can do it for the ones
I have? Thank you!

On Wed, October 29, 2014 9:18 pm, Zachary Greenberg wrote:
> Hi Rich,
>
> Do you have a post-operative CT scan of your ECoG patient? If you have
> that
> and a high-res T1, you can get very accurate reconstruction of electrode
> positions on the brain surface by corregistering the two.
>
> -zack
>
> On Wed, Oct 29, 2014 at 3:32 PM, rwlodar2@uic.edu <rwlodar2@uic.edu>
> wrote:
>
>> Hello my names Rich. I am working on a project that involves creating 3D
>> models of patient brains and placing ECoG (Electrocorticography) leads
>> on
>> these models. I have intra-operative pictures of the leads placed on the
>> subjects and I'm using these pictures to attempt to accurately place the
>> leads. However, as you might guess, the 3D models are very different
>> from
>> looking at a live brain and the true sulcal and gyral pattern is
>> difficult
>> to determine from the pictures. I was wondering if it is possible to
>> have
>> freesurfer create or mark, in some way, the veins on the models so that
>> I
>> can use the venous system as points of reference when placing the leads.
>> If not, is there a better way to do so that you can think of? I am
>> relatively new to freesurfer so I don't fully understand its capability
>> yet. Thanks!!
>>
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>
> --
> *Zachary Greenberg*
> *Assistant Imaging Specialist*
> *Department of Neurological Surgery*
> *University of California, San Francisco*
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