The relative position of the head with respect to the MEG sensors changes every time a new session begins and the subject is placed inside the MEG machine. To keep track of the position, the channel locations are given with respect to 3 fiducials (markers) placed at the nasion point, the left and the right ear. When we import a new MRI scan, we need to define these 3 points in the MR volume so that the anatomical information will correspond to the configuration of the subject during the MEG session. Transforming the MR volume into the channel coordinate system is achieved by defining a Subject Coordinate System (SCS). Further, all tessellated surfaces imported in BrainStorm need the SCS to be properly aligned.

In this section we will import MRI Data into BrainStorm and define a SCS by specifying 3 fiducial points: nasion, left ear, and right ear.

• Go to BST Main window ->Tools -> MRI Tool. This will open a window called MRI Viewer.

• On MRI Viewer window, go to MRI File-> Import-> Import .mri[CTF].
• Choose somMRI.mri file, and you should be able to see the scan in the MRI Tool. Hint: A window called SCS Specification should open, too.

	Fiducial points are already defined for this demo file. If you can't see the defined points follow the steps given below:
	Go to View->Lock Views and View->Add Crosshair to be able to lock all 3 views and see the crosshairs on the scans. Locate the nasion point in the sagittal, coronal and axial views and click Select to define this point. Repeat for left ear and right ear.

• Assign the points properly on the SCS Specification window and click Done when finished. Hint: Make sure you have selected the correct coordinate system (CTF/Magnes or Neuromag). If SCS Specification window did not open go to Image Coordinates menu item on MRI Viewer window and select Define Fiducials.

• Save the resulted MR Scans in BrainStorm format using the pop-up window called Save Anatomical Scans in... In somDemo_av_Subject directory, type somDemo inside the filename field and click Save.
• You should see the MRI oriented properly in the MRI Tool.

The file somDemo_subjectimage.mat has been created in the C:\BSTDemoData\Subject folder. It contains the anatomy of the subject and the Subject Coordinate System (SCS) structure in BrainStorm format.

Previous  Contents   Next