mne-python scale mri
DESCRIPTION
Scaling a template MRI and coregistering it to a subject's head shape.TRANSCRIPT
Coregistration in mne-pythonSubjects without MRI
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 MNE-Python; please report unexpected behavior to the mne-analysis mailing list
Overview
Select Raw File
Set MRI Fiducials
Select MRI Scale the MRI
Save the Result
Find Head Shape to MRI Co- registration
Control the 3D View
3D View
Input Files• Specify the directory containing MRI-
subjects (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.
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.
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 the forehead
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)
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
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
Saving• Finally hit the save button to save the
scaled MRI as well as the head-MRI transformation in a *-trans.fif file