Brain Innovation

Developer Guide (2.6) - The Format of VMR Files

VMR files contain high-resolution anatomical 3D data sets, typically containing the whole brain (head) of subjects. The intensity values are stored as a series of bytes. See the V16 format for a version storing each intensity value with two bytes (short integers). The VMR format contains a small header followed by the actual data followed by a second, more extensive, header. The current version of VMR files is "4", which is only slightly different from version 3 (as indicated below). Version 3 added offset values to format 2 in order to represent large data sets efficiently, e.g. in the context of advanced segmentation processing. Compared to the original file version "1", file versions 2 and higher contain additional header information after the actual data ("post-data header"). This allows to read VMR data sets with minimal header checking if the extended information is not needed. The information in the post-data header contains position information (if available) and stores a series of spatial transformations, which might have been performed to the original data set ("history record"). The post-header data can be probably ignored for custom routines, but is important in BrainVoyager QX for spatial transformation and coregistration routines as well as for proper visualization.

VMR Pre-Data Header

VMR Data

Each data element (intensity value) is represented in 1 byte. The data is organized in three loops:

DimZ
DimY
DimX

Note that the axes terminology follows the internal BrainVoyager (BV) format. The mapping to Talairach axes is as follows:

BV X front -> back = Y in Tal space
BV Y top -> bottom = Z in Tal space
BV Z left -> right = X in Tal space

VMR Post-Data Header

The first four entries of the post-data header are new since file version "3" and contain offset values for each dimension as well as a value indicating the size of a cube with iso-dimensions to which the data set will be internally "expanded" for certain operations. The axes labels are in terms of BrainVoyager's internal format. These four entries are followed by scan position information from the original file headers, e.g. from DICOM files. The coordinate axes labels in these entries are not in terms of BrainVoyager's internal conventions but follow the DICOM standard. Then follows eventually a section listing spatial transformations which have been eventually performed to create the current VMR (e.g. ACPC transformation). Finally, additional information further descries the data set, including the assumed left-right convention, the reference space (e.g. Talairach after normalization) and voxel resolution.

BYTES   DATA TYPE   DEFAULT      DESCRIPTION
2       short int   0            X offset (*1)
2       short int   0            Y offset (*1)
2       short int   0            Z offset (*1)
2       short int   256          Framing cube dimensions (*1)
4       int                      "PosInfosVerified" flag indicating whether info could be read from original file headers
4       int         1            Coordinate system entry, "1" = DICOM
4       float                    X coordinate of center of first slice
4       float                    Y coordinate of center of first slice
4       float                    Z coordinate of center of first slice
4       float                    X coordinate of center of last slice
4       float                    Y coordinate of center of last slice
4       float                    Z coordinate of center of last slice
4       float                    Slice row direction vector, x component
4       float                    Slice row direction vector, y component
4       float	 	                 Slice row direction vector, z component
4       float                    Slice column direction vector, x component
4       float                    Slice column direction vector, y component
4       float                    Slice column direction vector, z component
4       int                      Nr of rows of slice image matrix
4       int	 	                   Nr of columns of slice image matrix
4	      float	 	                 Extent of field of view (FoV) in row direction [mm]
4	      float	 	                 Extent of field of view (FoV) in column direction [mm]
4	      float	 	                 Slice thickness in mm
4	      float	 	                 Gap thickness in mm
4	      int	        0	           NrOfPastSpatialTransformations
                                 IF (NrOfPastSpatialTransformations > 0) list of past spatial transformations (*2)
1	      byte	       1	           Left-right convention (*3)    (modified in v4)
1	      byte	 	                  Reference space flag (*4)     (new in v4)
4	      float	 	                 Voxel resolution along x axis
4	      float	 	                 Voxel resolution along y axis
4	      float	 	                 Voxel resolution along z axis
1	      byte	 	                  flag (0, 1) indicating whether voxel resolution is verified
1	      byte	 	                  flag (0, 1) indicating whether Talairach space mm
4	      int	 	                   Min intensity value in original 16-bit data
4	      int	 	                   Mean intensity value in original 16-bit data
4	      int	 	                   Max intensity value in original 16-bit data

(*1) These four entries have been added in file version "3" with BrainVoyager QX 1.7. All other entries are identical to file version "2".

(*2) For each past transformation, the information specified in the following table is stored. The "type of transformation" is a value determining how many subsequent values define the transformation: value "1" - rigid body+scale (3 translation, 3 rotation and 3 scale values), value "2" - affine transformation (4x4 matrix), "4" - Talairach transformation, "5" Un-Talairach transformation.

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