Can you get it to display correctly on the pial surface in conformed space?

On 09/17/2014 08:04 PM, Zachary Greenberg wrote:
> Hello Freesurfer experts,
>
> I am having a tough time getting my pial surfaces into the correct
> anatomical space. I work with ECoG Patients, so we have pre-implant
> high resolution T1s (GE SPGR), and post-implant high resolution CTs
> that show the location of ECoG electrodes within the patient's skull.
> Our goal: display ECoG electrodes in their correct positions on the
> patient's native pial surface.
>
> Right now, my pipeline works like this:
> -ACPC align the T1, leave it in LAS orientation.
> -recon-all the acpc T1, using -3T -all -openmp 8 -use-gpu
> -corregister the CT to the acpc T1 (SPM), get electrode coords in T1 space
> -plot the electrodes on the resultant .pial surface from freesurfer
>
> The problem is, I can definitely tell that the position of the pial
> mesh is off (probably by 10 millimeters or so), as the electrodes
> (which have the correct coordinates from the T1 correg, confirmed
> visually by overlaying the CT on T1) are not in their correct
> positions on the mesh. Likewise, DTI fibers reconstructed from EPIs
> correctly corregistered to the T1 also appear off position within the
> .pial mesh.
>
> Here is what I have tried:
>
> compute the transform from .pial to .pial.native as suggested on
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
>
> tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat --noedit --regheader
> mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname
> This results in a mesh that is flipped (left is right) and rotated
> such that anterior is inferior (frontal cortex is pointing downward).
> The mesh appears this way when plotted in any viewer besides
> freesurfer (MATLAB mesh, Pyqt) but appears in the correct orientation
> in freeview. Replacing orig.mgz with the original T1.nii in the
> command above produces the opposite effect, freeview plots the
> orientation wrong, and any other viewer plots the Mesh oriented
> correctly, and the mesh appears to be identical to the originally
> output .pial mesh (electrodes are still wrong).
>
> Any help in pin pointing what is going wrong here would be greatly
> appreciated. I have a feeling it has something to do with the mesh
> being in surface RAS and the original T1 being in LAS.
>
> Thanks a bunch,
> -Zack
>
>
>
>
>

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