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Coregistration in mne-python
Subjects without 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
•

Use “Fit LPA/RPA” to find an
initial approximate alignment
Coregistration
•

Head shape and MRI are
initially aligned at the nasion.

Adjust the nasion alignment to
properly align t...
Coregistration
•

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

Select the desired number of
scaling parameters (scaling
with the same factor along all
axes or scaling with a ...
Coregistration
•

Once a proper scaling factor is found,
use the fitting function that don’t scale
the MRI as well as manua...
Saving
•

Finally hit the save button to save the
scaled MRI as well as the head-MRI
transformation in a *-trans.fif file
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MNE-Pythyon Scale MRI

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MNE-Pythyon Scale MRI

  1. 1. Coregistration in mne-python Subjects without 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 • Select the template brain to use. The default template that comes with freesurfer and MNE is fsaverage. The fsaverage files can be copied into the subjects directory with the “Copy FsAverage to Subject Folder” button (the button does not work if a subject named “fsaverage” already exists). • Fsaverage comes with fiducials which should be automatically loaded, in which case you can skip 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 • Use “Fit LPA/RPA” to find an initial approximate alignment
  7. 7. Coregistration • Head shape and MRI are initially aligned at the nasion. Adjust the nasion alignment to properly align the forehead
  8. 8. 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)
  9. 9. Scaling • Select the desired number of scaling parameters (scaling with the same factor along all axes or scaling with a separate factor for the X, Y and Z axes) • Use the automatic fitting functions as well as manual adjustment to find a proper MRI scaling factor
  10. 10. Coregistration • Once a proper scaling factor is found, use the fitting function that don’t scale the MRI as well as manual adjustment to fine tune the coregistration
  11. 11. Saving • Finally hit the save button to save the scaled MRI as well as the head-MRI transformation in a *-trans.fif file

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