dmr.tff

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

# TextFileFormat (leave this tag as magic token!)

# BVQX file format for *.DMR files (Diffusion MR data)
# DMR FileVersions supported: 1, 5
#
# Version:  v0.7a
# Build:    7082720
# Date:     Aug-27 2007, 8:15 PM CEST
# Author:   Jochen Weber, Brain Innovation, B.V., Maastricht, NL
# URL/Info: http://wiki.brainvoyager.com/BVQXtools

# FILE FORMAT
Description:Diffusion MRI files
Extensions:dmr
FieldDelimiters: {[32]}
LineDelimiters: {[13, 10], [10]}
ParagraphArrays:0
SkipEmptyLines:1
Magic:|
name          |range       |type    |magic
DMR_grddir    |1, 2048     |regexpi |gradientdirectionsverified\:\s*(yes|no)
EndMagic

# FIELDS
ListOfFields:!
type !cond               !field               !datatype!format !dim    !default !varname
WRTLN!!!!!!!  # empty line

# on read, check file version before attempt
FIELD!                   !FileVersion            !double  !%d     !1      !1       !FileVersion
FLIST!                   !NrOfVolumes            !double  !%d     !1      !        !NrOfVolumes
FLIST!                   !NrOfSlices             !double  !%d     !1      !        !NrOfSlices
FLIST!                   !NrOfSkippedVolumes     !double  !%d     !1      !        !NrOfSkippedVolumes

# Data link
FIELD!                   !Prefix                 !string  !"%s"   !1      !        !Prefix
FIELD!                   !DataStorageFormat      !double  !%d     !1      !        !DataStorageFormat

# Header fields
FLIST!                   !TR                     !double  !%d     !1      !        !TR
FLIST!                   !InterSliceTime         !double  !%d     !1      !        !InterSliceTime
FLIST!                   !TimeResolutionVerified !double  !%d     !1      !        !TimeResolutionVerified
FLIST!                   !TE                     !double  !%d     !1      !        !TE
FLIST!                   !SliceAcquisitionOrder  !double  !%d     !1      !        !SliceAcquisitionOrder
FLIST!                   !SliceAcquisitionOrderVerified !double !%d !1    !        !SliceAcquisitionOrderVerified
FIELD!                   !ResolutionX            !double  !%d     !1      !        !ResolutionX
FIELD!                   !ResolutionY            !double  !%d     !1      !        !ResolutionY
FLIST!                   !LoadAMRFile            !string  !"%s"   !1      !        !LoadAMRFile
FLIST!                   !ShowAMRFile            !double  !%d     !1      !        !ShowAMRFile
FLIST!                   !ImageIndex             !double  !%d     !1      !        !ImageIndex
FLIST!                   !LayoutNColumns         !double  !%d     !1      !        !LayoutNColumns
FLIST!                   !LayoutNRows            !double  !%d     !1      !        !LayoutNRows
FLIST!                   !LayoutZoomLevel        !double  !%d     !1      !        !LayoutZoomLevel
FLIST!                   !SegmentSize            !double  !%d     !1      !        !SegmentSize
FLIST!                   !SegmentOffset          !double  !%d     !1      !        !SegmentOffset
FIELD!@FileVersion > 4   !NrOfLinkedProtocols    !double  !%d     !1      !1       !NrOfLinkedProtocols
EXPRE!$TFFREAD && @FileVersion < 5 !!!!!!@NrOfLinkedProtocols = 1;
FIELD!                   !ProtocolFile           !string  !"%s"   !1      !        !ProtocolFile

# Internal resolution
FIELD!                   !InplaneResolutionX     !double  !%f     !1      !        !InplaneResolutionX
FIELD!                   !InplaneResolutionY     !double  !%f     !1      !        !InplaneResolutionY
FIELD!                   !SliceThickness         !double  !%f     !1      !        !SliceThickness
FIELD!                   !SliceGap               !double  !%f     !1      !        !SliceGap
FIELD!                   !VoxelResolutionVerified!double  !%d     !1      !        !VoxelResolutionVerified

# Position information
WRTLN!!!!!!!  # empty line
WRTLN!!!!!!!  # empty line
WRTLN!!!!!!!PositionInformationFromImageHeaders
WRTLN!!!!!!!  # empty line
FIELD!                   !PosInfosVerified       !double  !%d     !1      !0       !PosInfosVerified
FIELD!                   !CoordinateSystem       !double  !%d     !1      !0       !CoordinateSystem
FLIST!                   !Slice1CenterX          !double  !%8.5f  !1      !        !Slice1CenterX
FLIST!                   !Slice1CenterY          !double  !%8.5f  !1      !        !Slice1CenterY
FLIST!                   !Slice1CenterZ          !double  !%8.5f  !1      !        !Slice1CenterZ
FLIST!                   !SliceNCenterX          !double  !%8.5f  !1      !        !SliceNCenterX
FLIST!                   !SliceNCenterY          !double  !%8.5f  !1      !        !SliceNCenterY
FLIST!                   !SliceNCenterZ          !double  !%8.5f  !1      !        !SliceNCenterZ
EXPRE!1 == 0 !!!!!!; # needed for MATLAB R13, regexp/i bug with too long pattern
FLIST!                   !RowDirX                !double  !%f     !1      !        !RowDirX
FLIST!                   !RowDirY                !double  !%f     !1      !        !RowDirY
FLIST!                   !RowDirZ                !double  !%f     !1      !        !RowDirZ
FLIST!                   !ColDirX                !double  !%f     !1      !        !ColDirX
FLIST!                   !ColDirY                !double  !%f     !1      !        !ColDirY
FLIST!                   !ColDirZ                !double  !%f     !1      !        !ColDirZ
EXPRE!1 == 0 !!!!!!; # needed for MATLAB R13, regexp/i bug with too long pattern
FLIST!                   !NRows                  !double  !%d     !1      !        !NRows
FLIST!                   !NCols                  !double  !%d     !1      !        !NCols
FLIST!                   !FoVRows                !double  !%d     !1      !        !FoVRows
FLIST!                   !FoVCols                !double  !%d     !1      !        !FoVCols

# Must be fields (no colon!)
FIELD!                   !SliceThickness         !double  !%f     !1      !        !SliceThickness
FIELD!                   !GapThickness           !double  !%f     !1      !        !GapThickness

WRTLN!!!!!!!  # empty line
WRTLN!!!!!!!  # empty line
FIELD!                   !NrOfPastSpatialTransformations!double !%d !1    !        !NrOfPastSpatialTransformations

# If past transformations
EXPRE!$TFFREAD      !!!!!!@Trf = cell2struct(cell(0, 0, 5), {'NameOfSpatialTransformation', 'TypeOfSpatialTransformation', 'AppliedToFile', 'NrOfTransformationValues', 'TrfMatrix'}, 3);
BLOOP!@NrOfPastSpatialTransformations > 0 !PastST!!!@NrOfPastSpatialTransformations !!PastST
FLIST!                   !NameOfSpatialTransformation !string !"%s"!1     !        !Trf($PastST).NameOfSpatialTransformation
FLIST!                   !TypeOfSpatialTransformation !string !%d !1      !        !Trf($PastST).TypeOfSpatialTransformation
FLIST!                   !AppliedToFile          !string  !"%s"   !1      !        !Trf($PastST).AppliedToFile
FLIST!                   !NrOfTransformationValues!double !%d     !1      !        !Trf($PastST).NrOfTransformationValues
ARRAY!@Trf($PastST).TypeOfSpatialTransformation == 1 !TrfMatrix!double !%.6f !3, 3 !Trf($PastST).TrfMatrix
ARRAY!@Trf($PastST).TypeOfSpatialTransformation == 2 !TrfMatrix!double !%.6f !4, 4 !Trf($PastST).TrfMatrix
ARRAY!@Trf($PastST).TypeOfSpatialTransformation >  2 !TrfMatrix!double !%.6f !3, 3 !Trf($PastST).TrfMatrix
ELOOP!                   !PastST           !!!  !!PastST

# otherwise
WRTLN!@NrOfPastSpatialTransformations == 0 !!!!!!  # empty line
WRTLN!@NrOfPastSpatialTransformations == 0 !!!!!!  # empty line

# Convention and first data file
FIELD!                   !RadiologicalConvention !string  !%s     !1      !YES     !RadiologicalConvention
WRTLN!!!!!!!  # empty line
WRTLN!!!!!!!  # empty line
FIELD!                   !FirstDataSourceFile    !string  !"%s"   !1      !        !FirstDataSourceFile

# Gradient information
BLOOP!@FileVersion < 5   !IsFV1To4               !        !       !1      !        !IsFV1To4
FIELD!                   !GradientDirectionsVerified!string !%s   !1      !YES     !GradientDirectionsVerified
FIELD!                   !GradientXDirInterpretation!double !%d   !1      !1       !GradientXDirInterpretation
FIELD!                   !GradientYDirInterpretation!double !%d   !1      !3       !GradientYDirInterpretation
FIELD!                   !GradientZDirInterpretation!double !%d   !1      !5       !GradientZDirInterpretation
FIELD!                   !GradientInformationAvailable!string !%s !1      !YES     !GradientInformationAvailable
EXPRE!$TFFREAD && ~strcmpi(@GradientInformationAvailable, 'yes') !!!!!!@GradientInformation = [];
ARRAY!strcmpi(@GradientInformationAvailable, 'yes')!GradientInformation!double !%f !@NrOfVolumes, 4 ! !GradientInformation
ELOOP!                   !IsFV1To4               !        !       !       !        !IsFV1To4

# try to read DWI data
EXPRE!$TFFREAD      !!!!!!@DWIData = []; dtsf = @DataStorageFormat; if dtsf > 1, [dmrf{1:3}] = fileparts($FILENAME); dwif = ''; dwisz = []; tname = [dmrf{1} '/' dmrf{2} '.dwi']; if exist(tname, 'file') == 2, dwif = tname; else, tname(end-2:end) = 'DWI'; if exist(tname, 'file') == 2, dwif = tname; end, end, if ~isempty(dwif), nov = @NrOfVolumes; nos = @NrOfSlices; rsx = @ResolutionX; rsy = @ResolutionY; switch(dtsf), case {2}, dwisz = [rsx, rsy, nov, nos]; case{3}, dwisz = [rsx, rsy, nos, nov]; case{4}, dwisz = [nov, rsx, rsy, nos]; end, end, if ~isempty(dwisz), try, @DWIData = transio(dwif, 'ieee-le', 'uint16', 0, dwisz); end, end, end
EXPRE!$TFFWRITE     !!!!!![dmrf{1:3}] = fileparts($FILENAME); if any(dmrf{3}(2:end) == upper(dmrf{3}(2:end))), dmrf{3} = '.DWI'; else, dmrf{3} = '.dwi'; end, dwif = [dmrf{1} '/' dmrf{2} dmrf{3}]; try, dwid = @DWIData; if istransio(dwid), tios = struct(dwid); if ~strcmpi(tios.FileName, dwif), if ~cpfile(tios.FileName, dwif, 1); error('FILE_COPY_ERROR'); end, @DWIData = transio(dwif, 'ieee-le', 'uint16', 0, tios.DataDims); end, elseif ~isempty(dwid), dwii = fopen(dwif, 'w', 'ieee-le'); if dwii < 1, error('FILE_OPEN_ERROR'); end, fwrite(dwii, @DWIData(:), 'uint16'); fclose(dwii); end, catch, error('Error saving DWI data to new file.'); end
# end of fields
EndListOfFields

NewFileCode:!
@FileVersion = 1;
@NrOfVolumes = 1;
@NrOfSlices = 64;
@NrOfSkippedVolumes = 0;
@Prefix = 'untitled-';
@DataStorageFormat = 3;
@TR = 8000;
@InterSliceTime = @TR / @NrOfSlices;
@TimeResolutionVerified = 0;
@TE = 2 * round(@InterSliceTime / 3);
@SliceAcquisitionOrder = 0;
@SliceAcquisitionOrderVerified = 0;
@ResolutionX = 128;
@ResolutionY = 128;
@LoadAMRFile = '<none>';
@ShowAMRFile = 0;
@ImageIndex = 0;
@LayoutNColumns = 6;
@LayoutNRows = fix(0.99 + @NrOfSlices / @LayoutNColumns);
@LayoutZoomLevel = 1;
@SegmentSize = 10;
@SegmentOffset = 0;
@ProtocolFile = '<none>';
@InplaneResolutionX = 2;
@InplaneResolutionY = 2;
@SliceThickness = 2;
@SliceGap = 0;
@VoxelResolutionVerified = 0;
@PosInfosVerified = 0;
@CoordinateSystem = 1;
@Slice1CenterX = 0;
@Slice1CenterY = 0;
@Slice1CenterZ = -(@NrOfSlices - 1) * (@SliceThickness + @SliceGap) / 2;
@SliceNCenterX = 0;
@SliceNCenterY = 0;
@SliceNCenterZ = (@NrOfSlices - 1) * (@SliceThickness + @SliceGap) / 2;
@RowDirX = 1;
@RowDirY = 0;
@RowDirZ = 0;
@ColDirX = 0;
@ColDirY = 1;
@ColDirZ = 0;
@NRows = @ResolutionX;
@NCols = @ResolutionY;
@FoVRows = @NRows * @InplaneResolutionX;
@FoVCols = @NCols * @InplaneResolutionY;
@GapThickness = @SliceGap;
@NrOfPastSpatialTransformations = 0;
@Trf = cell2struct(cell(0, 0, 5), {'NameOfSpatialTransformation', 'TypeOfSpatialTransformation', 'AppliedToFile', 'NrOfTransformationValues', 'TrfMatrix'}, 3);
@RadiologicalConvention = 'YES';
@FirstDataSourceFile = '<none>';
@GradientDirectionsVerified = 'YES';
@GradientXDirInterpretation = 1;
@GradientYDirInterpretation = 3;
@GradientZDirInterpretation = 5;
@GradientInformationAvailable = 'NO';
@GradientInformation = zeros(@NrOfVolumes, 4);
@DWIData = [];
EndNewFileCode