BrainVoyager version: 22.4.4
Dataset used: NeWBI data, sub-04: https://openneuro.org/search/newbi4fmri
Please note: The method described below can be applied to any set of POIs defined on a standard SPH mesh (assuming these POIs should be visualized/aligned to another standard SPH mesh (of the same resolution)
It is very helpful to obtain automatic labelling of cortical structures in a specific surface reconstruction. BrainVoyager offers an option to use predefined patches of interest (POIs) in combination with cortex-based alignment to make optimal use of a couple of standard POIs coming with the standard installation (available in the AtlasCortex folder of the BrainVoyager installation directory).
When not including the cortex based alignment information into the POI labelling, any predefined area – which is based on a specific anatomy - will not fit very well to another subject-specific cortex.
1. The problem
To demonstrate the mismatch, we overlay the predefined POIs on a surface reconstruction of another brain. All necessary information can be found in the AtlasCortex folder of the BrainVoyager installation directory:
The folder contains several POI files as well as curvature maps necessary for cortex based alignment.
To check the current status of overlap between the predefined BrainVoyager POIs and a specific anatomy, we load a standard-resolution SPH mesh that was created based on the MPRAGE data of subject sub-04 of the NeWBI 4 fMRI data. Please note that it has to be a standard-resolution SPH mesh, because the BrainVoyager POIs have been defined on the basis of a standard mesh. In addition we load one of the POI files in the Atlas Cortex folder, e.g. CG_Gyri_LH.poi.
We choose a structure within the POI file, e.g. the precentral gyrus, clicking the “Show POIs” button, we display it on the currently created mesh. We can see clearly that the precentral gyrus POI is not properly aligned to the cortical folding pattern of subject sub-04.
To optimally use the POI labels in the Atlas brains folder, we have to use the cortex- based alignment technique.
2. Using cortex-based alignment to improve the overlap with standard POIs
First we load a hemisphere we would like to align to the atlas brain. We open the left hemisphere representation of subject sub-04 (sub-04_ses-01_T1w_IIHC_MNI_WM_LH_RECOSM_SPH.srf) and navigate to the cortex based alignment dialog.
The following processing steps depend on the current status of data processing. If the data has not yet been used in cortex-based alignment, one has to create and process the corresponding files first (Sphere, SPH file).
In this case, we have already prepared the data and may start directly with the alignment between source(s) and target. We open the “Target Sphere” tab and load the prepared SMP file of the left hemisphere of subject “CG” (from the “AtlasCortex” folder) and click the “Create PMP” button.
We open the “Align group” tab an use the “Add” button to Add the curvature SMP of subject sub-04. We choose the option to “Align each entry to target sphere” and click on "Go"
After the alignment is performed, we open the "Align Pair" tab and click the “Copy Labels…” button. In the appearing dialog we have to specify three different files:
1. the POI file from the AtlasCortex folder that we would like to visualize and align to sub-04.
2. the source SPH mesh from sub-04 that was aligned to the cortical curvature of CG and that we would like to use to display the areas of interest
3. the sphere-to-sphere mapping file, which has just been created during the aligment. Because we have used the CG curvature as the target of the CBA, we have to use the “INV.ssm” file.
By clicking the “Copy” button, we create a new POI file that is based on the old POI file and the cortex-based alignment result (SSM file). This resulting POI file, “CG_Gyri_LH_Copied.poi”, is automatically presented.
We check again the position of the precentral gyrus by using the "Show POIs" button and can see an improvement in the correspondence of the POI with the individual curvature of subject sub-04: