[FieldTrip] Align freesurfer surface to headmodel

[Dorothy Sincasto]

Dear fieldtrippers

I would like to align the headmodel of a subject with the
freesurfer surface. It seems that this is a bit different than the
fieldtrip mne tutorial, as we already have the freesurfer surfaces  (so we
did not align the mri, save them and run freesurfer).

To try to convert the freesurface surface coordinates to the subjects MEG
coordinates I do:



cfg = [];

cfg.method = 'interactive';

cfg.coordsys = 'spm';

mri_spm    = ft_volumerealign(cfg, mri);



cfg            = [];

cfg.resolution = 1;

cfg.dim        = [256 256 256];

mri_spm_rs     = ft_volumereslice(cfg, mri);

transform_vox2spm = mri_spm_rs.transform;



cfg          = [];

cfg.method   = 'interactive';

cfg.coordsys = 'ctf';

mri_ctf_rs   = ft_volumerealign(cfg, mri_spm_rs);

transform_vox2ctf = mri_ctf_rs.transform;



T = transform_vox2ctf/transform_vox2spm;

sourcespace = ft_read_headshape({my_surface}

sourcespace = ft_transform_geometry(T, sourcespace);

However, although the surface and headmodel is quite aligned, the surface
is a bit lower and posterior than the headmodel, as can be seen in this
screenshot: https://ibb.co/eEVV2K

We also tried the transformation matrices from freesurfer outputed with the
command mri_info surface.surf

voxel to ras transform:

               -1.0000   0.0000  -0.0000   131.6938

                0.0000   0.0000   1.0000  -111.6126

               -0.0000  -1.0000  -0.0000   157.1196

                0.0000   0.0000   0.0000     1.0000


voxel-to-ras determinant -1


ras to voxel transform:

               -1.0000  -0.0000  -0.0000   131.6938

                0.0000  -0.0000  -1.0000   157.1196

                0.0000   1.0000   0.0000   111.6126

               -0.0000  -0.0000  -0.0000     1.0000


But the results are worse. I am a bit desperate in finding a way to align
the surface without having to rerun freesurface on all the subjects.

Is there a method to properly align the freesurfer surface to the aligned
headmodel?

Thank you
Dorothy
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