BrainVoyager cortical flatmaps

BrainVoyager is loaded on lan347, one of the new fast computers which really enhances the program's graphics capabilities.  A hardlock has to be plugged into the parallel port before starting the program (check with Larry about scheduling a time to use the hardlock). 

Open the file depall_tal_sigma_rh_clean1.vmr in the /da/exp/training/BrainVoyager directory.  An already segmented right brain hemisphere will be displayed along with the 3D Tools dialog as shown below:  Go to the segmentation tab of the 3D Tools dialog set the range from 140-225, move the cursor into an area of white matter and click the Grow region button.  This will highlight in blue (voxel value of 240) the voxels within this range.  Next decrease the low end of  the range to 130 and hit the Expand button to extend the selected volume closer to the white matter boundary. It is also a good idea to "fill" the ventricles which can be done using the draw with mouse tool under the segmentation tab. Set the New Val to 235 which will cause voxels to be drawn in a yellow color.  Click through each layer in the coronal view (or transverse, sagittal , whichever is easiest) and fill in the ventricles with yellow. Next set the Min/Max inclusion range to 235/235 and click the Set range button. This will change all the yellow voxels to blue with a  value of 240.   Create a mask of this area by setting the Min/Max inclusion range to 1-225 and new value to 0, then hitting the Set range button. This will set all non-blue voxels to zero and use SaveAs to save this mask file with _mask extension.

 Click on the segmentation tab and in the border function's frame click the Dilate button.  This thickens  and smooths the white matter boundary slightly and removes small holes in the segmentation .  Next hit the Smooth button 3-4 times to smooth out the border outline and finally click on the Clear for rec. button. The Clear for rec. button is supposed to make sure that the subsequent reconstruction process creates a valid 2D surface (i.e. without moebius bands).  After these steps the image should look like:

The next step is one pass reconstruction. Open the Surface Module by clicking the Surf module button found under the 3D Coords tab of the 3D Tools dialog.  The following window is displayed:

and provides a good practice area for navigating around the image in the surface module.  Holding the left mouse button and dragging the cursor to the left/right moves the image to the left/right.  Pressing the CTRL and SHIFT buttons while holding the left mouse button and dragging the cursor up/down on the screen makes the image appear farther/closer.  The image can be rotated about about the screen vertical by using SHIFT, left mouse button, move cursor left/right; about screen horizontal using SHIFT, left mouse button, move cursor up/down; about normal to screen using CTRL, left mouse button, move cursor left/right.  For quick navigation press the "v" key and the following dialog window comes up:

Clicking on a brain view brings up that view for the image in the surface module window.  The view can also be changed using the translation and rotation sliders.

Now to continue with the cortical flattening,  invoke the create mesh dialog using the menu Meshes-> Create Surface and click on the Reconstruct button (proper default values have already been set).

After a few seconds the surface mesh appears looking like this:

This surface is then smoothed by bringing up the Mesh Morphing and Coloring dialog using the Meshes->Surface finding and flattening menu:

Check smoothing mode in the Morphing forces frame, verify default values of 0.07 for Smoothing force and 150 for NrOfIterations and click the Go button.  The resulting smoothed surface will serve as a reference for all future morphed versions of the mesh so it should be saved in a file with something like _ref in the name.  At this time a check should be made for errors in the surface reconstruction. A bridge error is located just above the origin in the image shown below.

By clicking the in the Mesh Toolbox one can turn on the MapSurfToVMR mode which enables clicking on the error in the depall_tal_sigma_rh_clean1__ref.srf image and seeing the corresponding location in the depall_tal_sigma_rh_clean1_WMmask_1.vmr image so that  the error can be corrected (see p. 6-19 in manual).  The offending sulci connections can be removed  or the volume beneath the bridge filled in using the drawing tool  in the segmentation tab of the 3D Tools dialog.  The corrected mask volume is saved and all the steps from saving the mask file to this point must be repeated in order to create a new corrected surface.

To add points to the mask use the draw with mouse tool with new value set to 235 for drawing in yellow (BrainVoyager stores image values in the range 0 to 225 and reserves 226-255 for color values).  After marking the volume you want to fill in yellow set the Min/Max range values to 235/235 and New value to 240 and click the set range button.  The yellow voxels will turn blue indicating their new values of 240.  The changed mask can now be saved. 

To remove points from the mask use the draw with mouse tool as above to mark the volumes to remove with yellow, then click the Use non-m. button (use non-marked) and the yellow voxels will be set to zero.  Alternatively, set the Min/Max range values to 235/235 and New value to 0 and click the set range button.

A useful feature is the ability to use the F10 button to toggle between the mask and the original image in order to decide whether to add or delete white matter in a particular volume.  Go to the the Spatial Transf. tab of the 3D Tools dialog and click the load button in the 3D-3D alignment frame and choose the depall_tal_sigma_rh_clean1.vmr image file.  Hit the F10 button to toggle to a overlay image as shown here (the boundary of the mask is marked by white dots):

The next step is to start inflating the surface so that eventually it can be unfolded into a flat surface. It's a good idea to check again for errors early in the inflation process.  Click in the "Use informations from file: check box in the Mesh Morphing and Coloring dialog (see above). This will open a file dialog where the _ref file should be chosen. Also check the Use reference mesh box.  Now with the _ref surface loaded check Inflation mode in the Mesh Morphing and Coloring dialog (see above), set the smoothing force to 0.4 and NrOfIterations to  200 and click Go.  This partial inflation helps to bring out errors (i.e. areas where sulci are improperly connected and form bridges in the inflated surface. 

After errors have been corrected (and checked at the 200/0.4 inflation) finish up the inflation with another 500 steps with a smoothing force of 0.8.

BrainVoyager 2000 supports automatic unfolding.  After the surface is fully inflated use Mesh->Surf Find & Flattening, Options and click on auto cut. The six cuts are automatically made in the surface. If the image goes all black then there are probably still significant errors in the segmentation. Go back and check.

Next click on Auto Unfold and the five unfolding vectors along with the coloring of the unfolding areas are placed on the surface.  If the five areas between the cuts aren't colored differently or the unfolding vectors aren't located approximately as shown then there are still errors in the segmentation. Go back and check (I've encountered a long tunnel that went beneath a cut). If two sides of a cut are the same color then there is a subsurface link between them.  Close the Options dialog and choose GO to start the unfolding process.  After the unfolding is complete use the view window navigation to flip the image over (shift key + left/right mouse drag).  Go back to the Mesh->Surf Find & Flattening, Options and uncheck the Show vectors option, then in the Mesh Morphing and Coloring dialog click on the Length distortion button to display distortions caused by the unfolding process:

The next process is to remove some of  the length distortions caused by the unfolding. This is set up by opening the Mesh Morphing and Coloring dialog using the Meshes->Surface finding and flattening menu and checking the smoothing mode, setting the smoothing force to 0.8, the surface reduction force to 0.01 and the number of iterations to 100. After 100 iterations set the distortion reduction force to 0.02 and run another 100 iterations.  Continue incrementing the distortion reduction force by 0.01 and running 100 iterations until a value between 0.05 and 0.1 is reached. Finally, clicking on the curvature button in the Mesh Morphing and Coloring dialog adds coloring indicating the curvature of the original cortex surface.

As described above for the error correction, clicking the    in the Mesh Toolbox turns on the MapSurfToVMR mode which enables clicking on any point in the above surface image and having the cross hairs moved to the corresponding point in the volume image.

Statistical results can be displayed on the flattened cortical map following these steps. If you have just run a 3D statistical model and the results are currently displayed in the volume image, start the surface module from the 3Dcoords->Surf module button and load the flattened cortical hemisphere using Meshes->Load Surface.  Choose Meshes->Surface finding and flattening menu and click the use imformation from file to load the appropriate surface reference for the displayed flattened cortical surface.  Next click the Readfunc button at the bottom of the dialog box and the statistical map will appear on the cortical surface as shown below:

If the volume image is still linked to the 3D volume time course (.VTC) file and the MapSurfToVMR icon is selected, clicking on any of the orange areas will bring up the average time plot for the voxels corresponding to the selected area.  If you have a previously saved statistical 3D map choose Analysis->Overlay  maps to open a dialog window.  Choose File->Load 3D map to load a previously created statistical map.  Then open the surface module and follow the steps described above.