BrainVoyager v22.0

MNI Normalization

Anatomical 3D data sets can be normalized to MNI space using the Template-Based Normalization dialog that can be invoked by clicking the Normalize To MNI Template Space item in the Volumess menu. Note that the input VMR should have been preprocessed with the intensity inhomogeneity correction procedure including brain extraction (indicated by the "_IIHC" substring in the preprocessed VMR file name). Besides producing a VMR file in MNI (or Talairach) space, MNI normalization also produces a spatial transformation (.TRF) file that can be used to transform functional (.FMR) data into MNI space (see below). Anatomical and functional MNI space normalization can also be performed by specifying corresponding normalization workflows when using the data analysis management tools.

There are unfortunately several variants of MNI space. Ad default, BrainVoyager uses the most widely used MNI-152 space indicated by the selected MNI-ICBM 152 option in the MNI target space variant field. This space is recommended for group studies. Another option is to select the MNI Colin 27 option which will normalize to a slightly different MNI space represented by the average of 27 anatomical scans of subject "Colin". Clicking the Info buttons will provide more information including a link to the original MNI/ICBM data sets. When turning off the MNI target space variant field, the input VMR will not be transformed in MNI space but will be aligned with the ICBM 452 target average brain used for template matching. Since this data set is always used for automatic (template matching based) normalization, the ICBM 452 option in the Use template field is always turned on and can not be deactivated.

Template-matching with the ICBM 452 target brain is started when clicking the GO button. Information about the progress of the procedure is reported in the Log pane. After a few seconds, the resulting brain is shown in the BrainVoyager main window. In order to allow verification of the normalization result, a blend of the contours of the normalized VMR with the template brain in MNI space is shown as a second VMR (see snapshot above). Using the standard VMR keyboard toggling shortcut (F8) or the respective Show primary VMR / Show secondary VMR options in the Spatial Transf tab of the 3D Volume Tools dialog, one can switch between the two views.

Internally the input VMR is alwasy transformed to the ICBM 452 template by mimimizing a cost function that reflects the match of the input VMR with the target VMR. From the ICBM 452 space, the final target MNI space is reached by adding an additional fixed transformation step to the obtained 12 parameter transformation matrix; this matrix concatenation step is not performed when deselecting the MNI target space variant field. Aligning to the ICBM 452 with subsequent addition of a transformation to the target space allows to create transformation files for multiple target spaces; in the current version 3 transformation files are stored in the folder of the input VMR with names containing the original VMR name followed by the substrings "[Input-VMR]_TO_MNI_a12.trf", "[Input-VMR]_TO_MNIColin27_a12.trf" and "[Input-VMR]_TO_ICBM452_a12.trf" that indicate the target spaces MNI-152, MNI-Colin27 and the non-MNI ICBM-452 space; the "a12" substring in the .TRF names indicates that the transformation matrix has been obtained by fitting 12 parameters. One can use the stored .TRF files to transform the input VMR - or another VMR in the same space - to one of the indicated target spaces without rerunning the normalization step. One of the output files, usually the "[Input-VMR]__TO_MNI_a12.trf" file, is also needed for transforming functional .FMR data into MNI space (see below).

Template matching with the ICBM 452 can also be used to transform an input VMR data set to (near) Talairach space when selecting the To Talairach Space option. In this case the ICBM 452 template is used for template matching as for MNI normalization but a ACPC and TAL step are appended to bring the data into near Talairach space. After running template matching, a "_mACPC.trf" and "_mACPC.tal" file is created that can be used to transform functional data into Talairach space when using the Create VTC dialog (see below). Since the resulting transformation files are not obtained with the classical landmark-based ACPC-TAL procedure, the transformation files and the resulting VMR file will be marked by adding letter "m" (e.g. "_mTAL.vmr") to the indicating that this Talairach transformation is the result of a template matching procedure. The resulting VMR file will usually be in a space that is close but not identical to a VMR file that has been normalized using the conventional Talairach procedure; most notably, the distance between the AC and PC point will usually not correspond to the standardized distance of a normal ACPC-TAL procedure.

When inspecting coordinates in a MNI normalized VMR data set, the coordinates are "MNI coordinates" since the origin (point with a zero value for the x, y and z coordinates, see snapshot above) is not set to the AC point as in Talairach space but to a point shifted slightly as has been described previously (Brett et al.).

MNI Normalization of FMR Data 

Functional .FMR data sets can be transformed into MNI space using the standard Create VTC dialog that can be invoked by clicking the Create Normalized VTC From FMR Data item in the Analysis menu. Furthermore, MNI-space VTCs can also be created using the FMR normalization workflow in the context of the data analysis management tools.

As with transformation of FMR data sets to other spaces, the input-FMR data set need to be specified in the Functional slice-based data file (FMR) field using the respective Browse button. Also the the FMR-VMR initial and fine-tuning alignment .TRF files need to provided in the FMR - VMR coregistration file 1 and FMR - VMR coregistration file 2 fields as usual. In order to prepare the dialog for MNI normalization, the To MNI option need to be selected (see arrow in snapshot above). This will adjust the dialog showing the 12 parameter MNI tranformation file (_MNI_a12.TRF) field (see arrow in the middle of the snapshot above); the TRF file stored as a result of MNI normalization of the hosting VMR data set needs to be specified here, usually the .TRF file with the name "[Input-VMR]_TO_MNI_a12.trf" or one of the other files described above. While the FMR-VMR alignment files will bring the functional data in the space of the hosting VMR, the 12-parameter transformation matrix contained in the MNI normalization file will further transform the data from the space of the hosting VMR to MNI space in the same way as has been done before with the anatomical data set. Internally all transformation matrices are concatenated and the transformation from the original FMR space to MNI space is performed in a single transformation step for each functional volume of the FMR data. The name of the output VTC file is shown in the Resultig VTC file field; note that the suggested name for the VTC data set contains the substring "_MNI" (see arrow in snapshot above) indicating that the resulting data will be normalized in MNI space.

The resulting VTC file can be linked to an individual VMR (e.g. "[Input-VMR]_MNI.vmr" or an average (template) VMR data set in MNI space. In the example snapshot above, the created MNI space VTC has been linked to the "ICBM452-IN-MNI152-SPACE_BRAIN.vmr" data set that is available in the "MNITemplates" sub-folder in the BrainVoyager installation directory. The snapshot also shows that the VTC Properties dialog (like the VMR Properties dialog) can be inspected to verify that the functional data is now in MNI space.

Copyright © 2020 Rainer Goebel. All rights reserved.