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COORDINATE SYSTEMS IN BRAINSTORM BrainStorm uses three types of coordinate systems, MRI Coordinate System (MCS), Cube coordinate system (CCS), and Subject Coordinate System (SCS). MCS and CCS are introduced to deal with the volume of MRI data, and impose conventions on the orientation of the MRI scan (see table). Their difference is that the former is in engineering units (mm), and the later is in voxel units (integers). We define two types of SCS, based on CTF and Neuromag conventions (see table). When processing MEG or EEG data, all structures (sensor locations, tessellated surfaces, and MRI scans) should be translated on the same SCS coordinate system. MEG data For MEG data, the sensor locations typically are already in CTF or Neuromag format, so no further processing is required. The users can then use the Tessellation Alignment Tool and the MRI Viewer to transform surfaces and MR volumes into SCS (the same format, CTF or Neuromag, as the sensors). This transformation requires the definition of 3 fiducials by the user: Nasion, Right Ear, and Left Ear. EEG data For EEG data, the user has the additional task of translating the sensor (channel) locations into the same SCS coordinate system as the surfaces and MRI volume. The overall procedure is as follows: First, choose the SCS coordinate system of preference: CTF or Neuromag? It makes no difference, choose any. Note: It make no difference whichever system you choose, just make sure to consistently use the same one for channels/surfaces/MR volume. Both vendors are for MEG data, however we actually use their conventions to define a coordinate system. We understand it is counter-intuitive to require MEG vendors to use EEG data, but it is only for the coordinate system. You can complete an EEG study without any use of MEG data, we only need the specification of the coordinate system. However, if both MEG and EEG data are available for the same subject, choose the appropriate coordinate system for both data. Surfaces and MR volumes are transformed into a common coordinate system, as described in the MEG case. Use the Tessellation Alignment Tool to transform the channels into the proper coordinate system, by pressing 'Align Channels'. Coordinate Systems Definitions
TRANSFORMATION BrainStorm creates a Subject Coordinate System (SCS), for CTF or Neuromag data according to the user's choice, from MRI Coordinate System (MCS) by using the following affine transformation: where R is the rotation matrix and T is the transformation vector and they are stored inside the SCS structure in *subjectimage.mat file under the subject folder. Hint: Type uiload in the Matlab command prompt and load the proper *subjectimage.mat file and see the variables under the SCS structure. See mri2scs and scs2mri for detailed information about transformations from MCS to SCS and SCS to MCS. |
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