I worked this out recently, and it is a bit complicated. Attached is a matlab function that can convert a register.dat file into a proper ras2ras transformation matrix that can be used in matlab. Be sure to read the help (you need to provide the "optional" input for correct results).

If M is the output of fs_read_regdat, it will be the transformation matrix from the ref image (T1) to the reg image (epi). So you would do this:

srf_epiVox = M*srfVert

Date: Mon, 27 Jul 2009 13:05:14 -0400 From: greve@nmr.mgh.harvard.edu To: praneeth.namburi@duke-nus.edu.sg CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Overlay surface onto EPI

These things are devilish to figure out, but I think I would try this instead:

srf_epiVox = inv(vox2ras_epi)*bbregMat*srfVert

doug

Praneeth Namburi wrote:

...

Hello Dr. Greve, I used the bbregister tool to register a BOLD EPI volume to the surface with the --init-fsl option. The result looks good in tkregister2. Using the resulting .dat file, I am trying to express the vertex coordinates of the surface in EPI voxel space (EPI volume: 128 x 128 x 36 matrix, limits: -64 to 64, -64 to 64 and -18 to 18).

Given the following 4x4 matrices, vox2ras_epi : vox2ras transformation matrix from the EPI volume header bbregMat : transformation matrix from the .dat file created from bbregister command

Given the vertices of the subject's surface (nVert x 4) : srfVert

I used the following transformation to express the surface in EPI voxel coordinates: srf_epiVox = srfVert * inv(bbregMat) * inv(vox2ras_epi)

When I view the results of this transformation in MATLAB, I can see that the above expression is incorrect. I used imagesc to show one slice of EPI and scatter to plot of all the vertices in that slice.

Can you please let me know what the mistake is? Am I applying the transformation in an incorrect coordinate space? Am I missing any transformations?

Looking forward for your reply. Thank you.

Yours Sincerely, Praneeth

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