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Load the MRI and "reslice" it
In this step, we simply put the right side of the MRI up. Skipping this step will result in mixed up slices and/or upside down image.
Code Block title ft_volumereslice mrif = '/path/and/filename/to/T1_mri.mgz'; % the file format could be one of many supported by fieldtrip. Native DICOM format works but is a bit slow to load. % read in the mri mri=ft_read_mri(mrif); % flip image so it looks upright cfg = []; cfg.method = 'flip'; mri_aligned = ft_volumereslice(cfg,mri);
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Note that if you have used freesurfer previously to segment your MRI, you can load the original mri stored in your freesurfer subjects' directory under SubjectName/orig/001.mgz |
Roughly align the MRI with the fiducials.
Improve realignment with headshape points.
Create a head model (3D surfaces for brain, skull and scalp)
Load and align a template grid to the headmodel
Plot the results and check
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