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Coregistration in mne-python
Subjects with MRI
General Notes
•

The GUI uses the traits library
which supports different
backends but seems to work
best with QT4 current...
Overview
Select MRI

Scale the MRI
3D View

Set MRI
Fiducials

Find Head Shape
to MRI Coregistration

Select Raw File
Cont...
Input Files
•

Specify the directory containing MRIsubjects (subjects_dir)

•

Select the Raw file for which to do the
core...
Fiducials
•

Select the fiducial you want to
modify, and then click on the
head model to specify the
position. Fiducials ar...
Coregistration
•

Since the MRI stems from the
same subject and thus has the
right size, make sure scaling is
off (“No sca...
Coregistration
•

In case the head shape
contains outlier points, head
shape points can be omitted
based on their distance...
Coregistration
•

The head shape and MRI are
initially aligned using the
Nasion; in order to modify the
initial alignment ...
Saving
•

Finally hit the save button to save the
head-MRI transformation in a *-trans.fif
file

•

When creating the forwar...
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MNE-Python Coregistration

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Instructions for head-MRI coregistration using the mne-python coregistration GUI.

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MNE-Python Coregistration

  1. 1. Coregistration in mne-python Subjects with MRI
  2. 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. 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. 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. 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. 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. 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. 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. 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

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