On 02/13/2017 09:59 AM, Ting Qi wrote:

Dear freesurfer experts,

I have some questions about the coordinates conversion, and the relationship between several types of coordinates.

First of all, I’d like to confirm whether the coordinates reported in the results summary are based on MNI305 space?

Which summary? From mri_glmfit-sim? That is in MNI305 space.

Second, I plan to combine multi-modalities data, therefore I would like to use the peak vertex in the surface as a seed to do additional volume-based analysis. I have the vertex index, vertex ras, MNI coordinates reported in the summary text, but how can I get the correct and corresponding volume coordinates in MNI space, particularly in MNI152?

These are always tricky things. First run recon-all on the MNI152 brain. Next, create a surface overlay file with my target voxel = 1 and everything else 0. See https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51127.html. Map this file from fsaverage the mni152 using mri_surf2surf. Once there, map the surface into the volume space using mri_surf2vol. You can threshold it there to determine where your voxel is.

I read the page about the freesurfer coordinate system, they mentioned several cases about the transformation, but I still cant figure out what is the correct way in my case. Moreover, I tried the mni305 to mni152, but when I double checked the coordinates in mni152 space, the peak was no longer corresponds to the region reported in the mni305 space. So I sure there must be something wrong.

Finally, would anyone offer me a explanation about the relationship between surface RAS, volume RAS, MNI* RAS, Vertex MNI, Volume MNI coordinates? It quite confused me.

All of this is in the coordinate system page. If you have more questions, please ask something specific.

Thanks in advance,

Best regards, Ting

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