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MNE-Python Coregistration
- 1. Coregistration in mne-python Subjects with MRI
- 2. General Notes • The GUI uses the traits library which supports different backends but seems to work best with QT4 currently. To make QT4 the default: • In Canopy: change Preferences/Python/PyLab backend • In a terminal: $ export ETS_TOOLKIT=“qt4” • The coregistration GUI is a recent addition to MNEPython; please report unexpected behavior to the mne-analysis mailing list
- 3. Overview Select MRI Scale the MRI 3D View Set MRI Fiducials Find Head Shape to MRI Coregistration Select Raw File Control the 3D View Save the Result
- 4. Input Files • Specify the directory containing MRIsubjects (subjects_dir) • Select the Raw file for which to do the coregistration • If it is not automatically selected, select the MRI subject • If a fiducials file is found in the MRI directory it is automatically loaded and you can skip the next slide. If not, load a file manually, or specify the fiducials as described on the next slide.
- 5. Fiducials • Select the fiducial you want to modify, and then click on the head model to specify the position. Fiducials are displayed as small colored spheres. • When all the fiducials are specified, save the positions so they can be loaded in the future. • Lock the fiducials to proceed to the coregistration.
- 6. Coregistration • Since the MRI stems from the same subject and thus has the right size, make sure scaling is off (“No scaling”) • Use LPA and RPA for an initial approximate alignment
- 7. Coregistration • In case the head shape contains outlier points, head shape points can be omitted based on their distance from the MRI head surface (for the sample data, 10 mm is a good distance)
- 8. Coregistration • The head shape and MRI are initially aligned using the Nasion; in order to modify the initial alignment use the translation parameters • Then use the automatic fitting functions and manual parameter adjustment to find a satisfactory coregistration
- 9. Saving • Finally hit the save button to save the head-MRI transformation in a *-trans.fif file • When creating the forward solution, specify this file as the mri argument