Importing Tessellation Surfaces

Import Tessellations

In this section we will import tessellation surfaces into BrainStorm and align them with the MEG sensor arrangement. We can later use these surfaces to create head models (cortical surface models , BEM models and others), apply Minimum-Norm solutions on the cortical surface, and visualize our results.

• Move all files (*.hdr, *.mri, *.hdr) from Subject folder into our current subject subfolder, called somDemo_av_Subject.
• It is important to notice that the subject file *brainstormsubject.mat does not link to the MRI scan we imported before (you can check it using uiload, as we described earlier). To fix this, go to Data Manager->Database->Edit -> Subjects(Anatomy) to open Subject Editor. Select somDemo_av in the Subject(s) in Database section. One anatomy file should be available, called somDemo_subjectimage.mat; BrainStorm has identified this file inside the subject folder, but has not assigned it to the subject file yet. Click Update to fix this. Now BrainStorm knows that the subject has an MRI scan and a SCS assigned to it. We can proceed by importing tessellations. Hint: To associate this subject to the current dataset: Go to Data Manager->Database->Edit -> Datasets(MEG/EEG) to open Study Editor. Select somDemo_av.ds/Brainstorm in the MEG/EEG data folders list box and somDemo_av Subject in Subjects listbox. Click Update and Done buttons. After doing this you can directly call Surface Manager from BST Main window (Tools-> Surface Manager).

• Click Surface Manager button to open the Surface Manager window. Select Import in the drop down menu called: Actions. On the pop-up window, select all tessellations you want to import (selection of all files, cortex.dfs, scalp.dfs, outer_skull.dfs, may be needed in the following sections) and click Done. BrainStorm will load all files and convert them into *_tess.mat files. You will be notified in the Messages window when the process is over. Hint: Realize that the comment for the tesselation is written after the filename. Ex: cortex_tess\cortex means that you have a file named cortex_tess.mat with comment 'cortex'. Realize that if you have more than one surface associated with a file you see all the surfaces (same filename with different comments).

• Select the cortex_tess in the Available Envelopes section and downsample it by selecting Downsize in the drop down menu Actions. Repeat this process for the other surfaces (scalp_tess, outer_skull_tess). Hint: Write 10000 in the Tessellation Downsizing pop-up window as the new number of vertices for the selected envelope. Downsizing is required if large surfaces are to be used for current density reconstruction at a later stage.

You should see 6 Tessellation files with proper descriptions. In the C:\BSTDemoData\Subject\somDemo_av_Subject directory you should see the same files (.mat files).

Aligning Tessellation Surfaces

Align Tessellations

Follow the instructions below to align the tessellation surfaces.

• Select all downsized surfaces; cortex_10000V_tess, outer_skull_10000V_tess, scalp_10000V_tess, in available envelopes section.
• Select Align in Actions drop down menu to open the Surface and Channel Alignment Tool and the Envelope Viz window. These windows are used to transform the tessellations into the Subject Coordinate System (SCS), i.e. align them with the MEG sensors.

• Click the Load Channels button to select a relevant channel file (BSTDemoData/Study/somDemo_av.ds/BrainStorm/somDemo_av_channel.mat). Notice that the tessellations are not aligned with the channels.
• Hide the channels by clearing the View check box next to Load Channels button.

• Use the buttons (Nasion/Left Ear/Right Ear) to select the corresponding fiducials on the scalp tessellation. A second click is required to register the selected point. Hint: You should define all 3 fiducials to align the surfaces. You can start rotating the figure after you select one of the fiducials or you ca use the Figure Toolbar to rotate the figure directly. Use Toggle Scene Light tool on Camera toolbar (View -> Camera Toolbar) if the tessellation is dark.
• Select CTF and click Align Surfaces button. 3 new .mat files are created: cortex_10000V_tess_CTF, outer_skull_10000V_tess_CTF,
  scalp_10000V_tess_CTF with the aligned surfaces.
• To verify the aligned channels: Close the Envelope Viz window, select aligned surfaces on Surface Manager and check the View box and click View. Finally View the channels on the Surface and Channel Alignment Tool to verify that the surfaces are now aligned with the channels.

• You can also check if these surfaces are aligned with the MRI. For that purpose, select cortex_10000V_tess_CTF in the Available Envelopes section and selectCheck Alignment with MRI in the Action drop down menu. You should see how your surfaces are aligned with the MRI in MRI Viewer. See the screenshot shown below as an example.

• You can change the transparency of the outer surfaces (such as head) to be able to see inner surfaces (such as brain). Hint: Controls for transparency, color, smoothness and curvature are on the Surface Manager window.

• At any time you can return to Surface Manager window to view the aligned surfaces. To do that select the aligned surfaces in the available envelopes list box and click View. Hint: To clear the surface(s) on the Envelope Viz window, clear the view box(es).

Quit the Surface and Channel Alignment Tool and Surface Manager to finish the procedure and click Done to in the Subject Editor to close it.

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