vmr.bff

toolbox of BVQX, This is the access between BV and matlab. It will help you to analysis data from BV

# BinaryFileFormat (leave this tag as its own magic token!)

# BVQX file format for *.VMR/*.V16 files (Volumetric MR dataset)
# VMR/V16 FileVersions supported: 0, 1, 2, 3
#
# VMR files contain anatomical 3D data stored as bytes. The VMR
# format version 2, which was designed for BrainVoyager QX in
# 2003, contains also the positioning data. An important point
# is that you understand how the three axes are ordered (see
# below).
#
# The positioning information is saved at the end of the file,
# after the actual data. 
#
# Intensity values ranging from 0 to 225 are gray scale values.
# Special color values are stored in the range 226-255.
#
# 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 
#
# Version:  v0.7
# Build:    7082720
# Date:     Aug-27 2007, 8:19 PM CEST
# Author:   Jochen Weber, Brain Innovation, B.V., Maastricht, NL
# URL/Info: http://wiki.brainvoyager.com/BVQXtools

# FILE FORMAT
Description:Volumetric anatomical MRI files,Volumetric anatomical MRI 16-bit files
EncodingSyntax:ieee-le
Extensions:vmr,v16

# FIELDS
ListOfFields:!
type  !cond                   !disktype!datatype!dim                      !default !varname

# although it costs some time, preset all fields!
EXPRE !$BFFREAD           !!!!!@@ = BVQXfile(0, 'newcont', 'vmr');

# Assume using a FileVersion tag
EXPRE !                   !!!!!$UFV = true;
EXPRE !$BFFREAD           !!!!!@FileVersion = 1;

# On read, check for FileVersion 1
FIELD !$BFFREAD               !uint16  !double  !1, 1                     !        !DimX
FIELD !$BFFREAD               !uint16  !double  !1, 1                     !        !DimY
FIELD !$BFFREAD               !uint16  !double  !1, 1                     !        !DimZ

# check filesize for VMR **and** V16 files
EXPRE !$BFFREAD           !!!!!if (@DimX * @DimY * @DimZ) == ($FILESIZE + 6), $UFV = false; end
EXPRE !$BFFREAD           !!!!!if (@DimX * @DimY * @DimZ) == (2 * $FILESIZE + 6), $UFV = false; end

# only allow FileVersion < 16
EXPRE !$BFFREAD           !!!!!if @DimX >= 16, $UFV = false; end

# which VMR version
EXPRE !$BFFREAD           !!!!!@VMR8bit = true; if ~isempty(strfind($EXTENSION, '16')), @VMR8bit = false; end

# rewind in any case
EXPRE !                   !!!!!fseek(fid, 0, -1);

# Handle NO FileVersion given -> only write VMRData
EXPRE !$BFFWRITE  !  !  !  !  !@VMR8bit = isempty(strfind(class(@VMRData), '16')); $OFV = @FileVersion; if ~@VMR8bit, @FileVersion = 1; end; try, if @FileVersion == 1, $UFV = false; end, catch, $UFV = false; end

# Reading first uint16, check for file version ...
FIELD !$UFV                   !uint16  !double  !1, 1                     !        !FileVersion

# If FileVersion is zero, we have to read NrOfCrossCorrLags
FIELD !@FileVersion == 0      !uint16  !double  !1, 1                     !0       !NrOfCrossCorrLags

# Setting up variables for writing ...
EXPRE !$BFFWRITE          !!!!!@DimX = size(@VMRData, 1);  # size taken from data
EXPRE !$BFFWRITE          !!!!!@DimY = size(@VMRData, 2);  # size taken from data
EXPRE !$BFFWRITE          !!!!!@DimZ = size(@VMRData, 3);  # size taken from data

# Read/write DimX, DimY, DimZ, VMRData
FIELD !                       !uint16  !double  !1, 1                     !        !DimX
FIELD !                       !uint16  !double  !1, 1                     !        !DimY
FIELD !                       !uint16  !double  !1, 1                     !        !DimZ
FIELD ! @VMR8bit              !uint8   !uint8   !@DimX, @DimY, @DimZ      !        !VMRData
FIELD !~@VMR8bit              !uint16  !uint16  !@DimX, @DimY, @DimZ      !        !VMRData

# Some additional fields for FileVersion 2
BLOOP !@FileVersion > 1       ! ! !1 ! !FileVersion2pp

# And yet some more fields in VMR FileVersion 3
BLOOP !@FileVersion > 2       ! ! !1 ! !FileVersion3pp
FIELD !                       !int16   !double  !1, 1                     !        !OffsetX
FIELD !                       !int16   !double  !1, 1                     !        !OffsetY
FIELD !                       !int16   !double  !1, 1                     !        !OffsetZ
FIELD !                       !uint16  !double  !1, 1                     !        !FramingCube
ELOOP !                       ! ! !  ! !FileVersion3pp

# Continuing with FileVersion 2 fields...
FIELD !                       !uint32  !logical !1, 1                     !        !PosInfoVerified
FIELD !                       !uint32  !double  !1, 1                     !        !CoordinateSystem
FIELD !                       !single  !double  !1, 1                     !        !Slice1CenterX
FIELD !                       !single  !double  !1, 1                     !        !Slice1CenterY
FIELD !                       !single  !double  !1, 1                     !        !Slice1CenterZ
FIELD !                       !single  !double  !1, 1                     !        !SliceNCenterX
FIELD !                       !single  !double  !1, 1                     !        !SliceNCenterY
FIELD !                       !single  !double  !1, 1                     !        !SliceNCenterZ
FIELD !                       !single  !double  !1, 1                     !        !RowDirX
FIELD !                       !single  !double  !1, 1                     !        !RowDirY
FIELD !                       !single  !double  !1, 1                     !        !RowDirZ
FIELD !                       !single  !double  !1, 1                     !        !ColDirX
FIELD !                       !single  !double  !1, 1                     !        !ColDirY
FIELD !                       !single  !double  !1, 1                     !        !ColDirZ
FIELD !                       !uint32  !double  !1, 1                     !        !NRows
FIELD !                       !uint32  !double  !1, 1                     !        !NCols
FIELD !                       !single  !double  !1, 1                     !        !FoVRows
FIELD !                       !single  !double  !1, 1                     !        !FoVCols
FIELD !                       !single  !double  !1, 1                     !        !SliceThickness
FIELD !                       !single  !double  !1, 1                     !        !GapThickness

# Read spatial transformation information
FIELD !                       !uint32  !double  !1, 1                     !        !NrOfPastSpatialTransformations
EXPRE !$BFFREAD           !!!!!@Trf = cell2struct(cell(0, 0, 5), {'NameOfSpatialTransformation', 'TypeOfSpatialTransformation', 'SourceFileOfSpatialTransformation', 'NrOfSpatialTransformationValues', 'TransformationValues'}, 3);
BLOOP !                       ! ! !@NrOfPastSpatialTransformations ! !NumTrf
FIELD !                       !cstring !cstring !1                        !        !Trf($NumTrf).NameOfSpatialTransformation
FIELD !                       !uint32  !double  !1, 1                     !        !Trf($NumTrf).TypeOfSpatialTransformation
FIELD !                       !cstring !cstring !1                        !        !Trf($NumTrf).SourceFileOfSpatialTransformation
FIELD !                       !uint32  !double  !1, 1                     !        !Trf($NumTrf).NrOfSpatialTransformationValues
FIELD !@Trf($NumTrf).TypeOfSpatialTransformation == 1!single!double!3, 3  !        !Trf($NumTrf).TransformationValues
EXPRE !$BFFWRITE & @Trf($NumTrf).TypeOfSpatialTransformation == 2!!!!!@Trf($NumTrf).TransformationValues = @Trf($NumTrf).TransformationValues';
FIELD !@Trf($NumTrf).TypeOfSpatialTransformation == 2!single!double!4, 4  !        !Trf($NumTrf).TransformationValues
EXPRE !$BFFREAD & @Trf($NumTrf).TypeOfSpatialTransformation == 2!!!!!@Trf($NumTrf).TransformationValues = @Trf($NumTrf).TransformationValues';
FIELD !@Trf($NumTrf).TypeOfSpatialTransformation >  2!single!double!@Trf($NumTrf).NrOfSpatialTransformationValues, 1!!Trf($NumTrf).TransformationValues
ELOOP !                       ! ! !  ! !NumTrf

# if no transformations, yet initialize field
EXPRE !@NrOfPastSpatialTransformations < 1!!!!!@Trf = cell2struct(cell(0, 0, 5), {'NameOfSpatialTransformation', 'TypeOfSpatialTransformation', 'SourceFileOfSpatialTransformation', 'NrOfSpatialTransformationValues', 'TransformationValues'}, 3);

# further fields
FIELD !                       !uint8   !double  !1, 1                     !        !Convention

# And yet some additional fields for more recent versions
FIELD !                       !single  !double  !1, 1                     !        !VoxResX
FIELD !                       !single  !double  !1, 1                     !        !VoxResY
FIELD !                       !single  !double  !1, 1                     !        !VoxResZ
FIELD !                       !uint8   !logical !1, 1                     !        !VoxResInTalairach
FIELD !                       !uint8   !logical !1, 1                     !        !VoxResVerified

# check resolutions (strange BV behavior...?)
EXPRE !$BFFREAD           !!!!!if all(abs([@VoxResX, @VoxResY, @VoxResZ] - 1) < 1e-5), @VoxResX = 1; @VoxResY = 1; @VoxResZ = 1; end, if all(abs([@VoxResX, @VoxResY, @VoxResZ] - 0.5) < 1e-5), @VoxResX = 0.5; @VoxResY = 0.5; @VoxResZ = 0.5; end

# in some cases there are extra fields even for version 2
BLOOP !@FileVersion > 2 || ($BFFREAD && ($FILESIZE - ftell(fid)) >= 12) || ($BFFWRITE && isfield(@@, 'MinOriginalValue')) ! ! !1 ! !FileVersion3pp2
FIELD !                       !int32   !double  !1, 1                     !        !MinOriginalValue
FIELD !                       !int32   !double  !1, 1                     !        !MeanOriginalValue
FIELD !                       !int32   !double  !1, 1                     !        !MaxOriginalValue
ELOOP !                       ! ! !  ! !FileVersion3pp2

# End of Loop @FileVersion > 1
ELOOP !                       ! ! !  ! !FileVersion2pp

# give VMR back as received
EXPRE !$BFFWRITE          !!!!!@FileVersion = $OFV;

# Read rest of File into REMAININGCONTENT
EXPRE !$BFFREAD           !!!!!$RemSize = $FILESIZE - ftell(fid);
EXPRE !$BFFWRITE          !!!!!$RemSize = 0; try, if isfield(@@, 'REMAININGCONTENT'), $RemSize = prod(size(@REMAININGCONTENT)); end, end
FIELD !$RemSize > 0           !uint8   !uint8   !1, $RemSize              !        !REMAININGCONTENT

# guess framingcube and offset if needed
EXPRE !$BFFREAD          !!!!!if all([@OffsetX, @OffsetY, @OffsetZ] == 0) && any([@DimX, @DimY, @DimZ] ~= @FramingCube), if @FileVersion < 3, if any([@DimX, @DimY, @DimZ] > 256), @FramingCube = 512; else, @FramingCube = 256; end, end, tfc = round(@FramingCube / 2); @OffsetX = floor(tfc - round(@DimX / 2)); @OffsetY = floor(tfc - round(@DimY / 2)); @OffsetZ = floor(tfc - round(@DimZ / 2)); end

# if V16 is available load/save it, too (if autov16 enabled)
EXPRE !$BFFREAD           !!!!![tfname{1:3}] = fileparts($FILENAME); if @VMR8bit && BVQXfile(0, 'config', 'vmr', 'autov16'), v16f = ''; tnlc = [tfname{1} '/' tfname{2} '.v16']; tnuc = [tfname{1} '/' tfname{2} '.V16']; if exist(tnlc, 'file') == 2, v16f = tnlc; elseif exist(tnuc, 'file') == 2, v16f = tnuc; end, if ~isempty(v16f), try, global bvqxclup; global bvqxcont; v16o = struct(BVQXfile(v16f)); v16l = v16o.L; v16c = bvqxcont(bvqxclup == v16l).C; if all([@DimX, @DimY, @DimZ] == [v16c.DimX, v16c.DimY, v16c.DimZ]), @VMRData16 = v16c.VMRData; BVQXfile(0, 'clearobj', v16l); end, catch, end, end, end
EXPRE !$BFFWRITE          !!!!![tfname{1:3}] = fileparts($FILENAME); v16l = []; v16f = [tfname{1} '/' tfname{2} '.v16']; if strcmpi(class(@VMRData), 'uint8') && strcmpi(class(@VMRData16), 'uint16') && BVQXfile(0, 'config', 'vmr', 'autov16') && numel(size(@VMRData)) == numel(size(@VMRData16)) && all(size(@VMRData) == size(@VMRData16)) && (~istransio(@VMRData16) || ~strcmpi(v16f, transiofilename(@VMRData16))), try, global bvqxclup; global bvqxcont; v16o = struct(BVQXfile('new:v16')); v16l = v16o.L; v16i = (bvqxclup == v16l); bvqxcont(v16i).C.FileVersion = 1; bvqxcont(v16i).C.DimX = @DimX; bvqxcont(v16i).C.DimY = @DimY; bvqxcont(v16i).C.DimZ = @DimZ; bvqxcont(v16i).C.VMR8bit = false; bvqxcont(v16i).C.VMRData = @VMRData16; Call(BVQXfile(0, 'makeobject', v16o), 'SaveAs', v16f); if istransio(@VMRData16), @VMRData16 = bvqxcont(v16i).C.VMRData; end, BVQXfile(0, 'clearobj', v16l); catch, if ~isempty(v16l), try, BVQXfile(0, 'clearobj', v16l); end, end; error(['Error saving V16: ' lasterr]); end, end
EndListOfFields

NewFileCode:!
# check which extension
if ~strcmpi(fftype, 'v16')
#
# for VMR files
@FileVersion = 3;
@DimX = 256;
@DimY = 256;
@DimZ = 256;
@VMR8bit = true;
@VMRData = uint8(0); @VMRData(256, 256, 256) = @VMRData(1);
@VMRData16 = [];
@OffsetX = 0;
@OffsetY = 0;
@OffsetZ = 0;
@FramingCube = 256;
@PosInfoVerified = false;
@CoordinateSystem = 1;
@Slice1CenterX = 0;
@Slice1CenterY = 0;
@Slice1CenterZ = -127.5;
@SliceNCenterX = 0;
@SliceNCenterY = 0;
@SliceNCenterZ = 127.5;
@RowDirX = 1;
@RowDirY = 0;
@RowDirZ = 0;
@ColDirX = 0;
@ColDirY = 1;
@ColDirZ = 0;
@NRows = 256;
@NCols = 256;
@FoVRows = 256;
@FoVCols = 256;
@SliceThickness = 1;
@GapThickness = 0;
@NrOfPastSpatialTransformations = 0;
@Trf = cell2struct(cell(0, 0, 5), {'NameOfSpatialTransformation', 'TypeOfSpatialTransformation', 'SourceFileOfSpatialTransformation', 'NrOfSpatialTransformationValues', 'TransformationValues'}, 3);
@Convention = 1;
@VoxResX = 1;
@VoxResY = 1;
@VoxResZ = 1;
@VoxResInTalairach = false;
@VoxResVerified = false;
@MinOriginalValue = 0;
@MeanOriginalValue = 127;
@MaxOriginalValue = 255;
#
# for V16 files
else
#
@FileVersion = 1;
@DimX = 256;
@DimY = 256;
@DimZ = 256;
@VMR8bit = false;
@VMRData = uint16(0); @VMRData(256, 256, 256) = @VMRData(1);
@VMRData16 = [];
@OffsetX = 0;
@OffsetY = 0;
@OffsetZ = 0;
@FramingCube = 256;
end
EndNewFileCode