You can also use bbregister to register the CT to the anatomical. I'm
not sure what steps beyond that you'd need to do.
doug
On 10/29/14 10:47 PM, Zachary Greenberg wrote:
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, rwlod...@uic.edu
<mailto:rwlod...@uic.edu> <rwlod...@uic.edu <mailto:rwlod...@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, rwlod...@uic.edu
<mailto:rwlod...@uic.edu> <rwlod...@uic.edu <mailto:rwlod...@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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>>
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>
>
> --
> *Zachary Greenberg*
> *Assistant Imaging Specialist*
> *Department of Neurological Surgery*
> *University of California, San Francisco*
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