BrainStorm

Important: Please read the coordinate system help file before proceeding below, to understand coordinate system conventions in BrainStorm.

In BrainStorm, all structures (surfaces, channels, and MR volume) of a subject must be in the same SCS. This tool allows the user to transform surfaces and channels; for transforming MR volumes please use the MRI Viewer. Further, in case you want to process an EEG study when MRI data are not available, you can use this tool to warp generic surfaces and MR volume to the subject (phantom study).

Typically, the user should load some tessellated surfaces (ie scalp and brain). Then, he should choose the scalp surface and assign markers on 3 points (nasion, left, and right ear). Then, he should choose CTF or Neuromag system (there is a slight difference between the definition of these two SCS coordinate systems), to match the coordinate system of the sensors. Clicking 'Align Tessellations' triggers an affine transformation (translation and rotation) for all surfaces for all loaded files. New files are generated with the transformed surfaces, with an additional tag 'alignedCTF' or 'alignedNeuromag'.

There is a strict requirement that all surfaces should be in actual dimensions, in meters; the affine transformation does not perform any scaling to change the size of the tessellations. Also, the tool assumes that all surfaces loaded simultaneously are in the same coordinate system. For example, if a scalp and brain surface are loaded, the transformation of the scalp (after selecting the fiducials) will be performed on the brain surface. Select view on all surfaces and inspect them simultaneously, to make sure they are on the same coordinate system (for example, by changing the transparency you should see the brain inside the scalp). To check if the surfaces are in meters, you can inspect them together with the channel structure (discussed below). This test works if the channel structure is in actual dimensions itself, otherwise both surfaces and channels will be on a wrong scale!

MEG/EEG channels can be loaded and visualized together with the loaded surfaces. Press the 'Load Channels' button, and locate the proper channel file. This file follows the format (*channel*.m), ie it is a brainstorm format channel file, and is located on the study directory (not the subject directory!). If the channels are in the wrong coordinate system, click 'Align Channels' to transform them into 'CTF' or 'Neuromag' coordinate system. This is typically not necessary for MEG data, because the channels are already aligned. But it is usually required for EEG data (The help file coordinate system discusses why we need MEG vendors for EEG data). After clicking 'Align Channels', select the 3 fiducials (nation, left/right preauricular) and the alignment will be performed. Inspect the channels with the aligned surfaces to make sure everything worked well.

in case you want to process an EEG study when MRI data are not available, you can use this tool to warp generic surfaces and an MR volume to the subject. First load the channel structure from the EEG study (see above). Then, align it with the CTF coordinate system (important) because the phantom is in this coordinate system. Initiate the warping procedure by pressing 'Phantom Study'. The 'channel assignment tool' pops up, while at the same time the phantom channels (red) are visible together with the EEG channels (yellow). If the EEG channels have tags compatible with the 10-20 coordinate system, click the button 'Autoassign (Tag)'. The assignments are displayed in the 'Tessellations' window with black lines. To simply match channels using Euclidean distance, use 'Autoassign (Dist)'. To manually assign channels, select them from the two lists (or click on the red / yellow points on the window) and click 'Assign'. To cancel the assignment, select the channels and click 'Deassign'. When several channels have been assigned (the assignment of nasion, and left/right preauricular points is required), click 'Go'. The files montreal_4layer_tess.mat and montreal_subjectimage.mat (located in the {bst home}\Phantom\montreal_subject directory) will be warped and saved in the current subject directory ({subject}_warped_4layer_tess.mat and {subject}_warped_subjectimage.mat ). You can load the warped surfaces and view them with the EEG channels. The channels should fall on the scalp surface if warping is successful. See a demonstration with video files here.

Click to select the NASION point on the scalp tessellation. The cursor becomes a crosshair to indicate that the tool is in point selection mode. A second click is required to register the selected point. Hint: First view a tessellation (e.g. Scalp or Head) to be able to locate a point on. You can rotate the figure using the Figure Toolbar. Use Toggle Scene Light tool on Camera toolbar (View -> Camera Toolbar) if the tessellation is dark. You should repeat the procedure every time you rotate the surface, because the new light source matches the current viewpoint of the user.

Click to select the LEFT EAR point on the scalp tessellation. A second click is required to register the selected point. See hints above.

Click to select the RIGHT EAR point on the scalp tessellation. A second click is required to register the selected point. See hints above.

Click to transform the tessellation into Subject Coordinate System (SCS), after selecting the fiducials, and the type of the coordinate system (CTF or Neuromag). New tessellation files will be generated, with the tag '*_CTF' or '*_Neuromag'.

Click to select a relevant channel file (MEG or EEG data). Hint: You should be able to find the appropriate channel information in the Study folder (where all MEG/EEG recordings are stored) in a subfolder called BrainStorm.

Aligns the loaded channel structure with the Subject Coordinate System (SCS). The user specifies 3 markers (Nasion, Right/Left-Preauricular) and the aligned channel overwrites the existing *channel*.mat file. It should typically used for EEG channel arrangements, when they are not in the proper coordinate system. The uses should specify CTF or Neuromag before channel alignment, so define the type of coordinate system of the tessellated surfaces and the MR volume.

Click to warp phantom surfaces and MR volume to the EEG channel file. This is useful when you have EEG data, but no MR is available. See above for description of the warping procedure.

Select the appropriate vendor for the MEG/EEG data. This option defines the coordinate system the surfaces and channels are going to be translated. See Subject Coordinate System (SCS) for details on CTF and Neuromag systems. In processing MEG or EEG data, all structures (channels, surfaces, and MRI volumes) should be transformed on the same coordinate system.