fmr.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 *.FMR files (Functional MR data)
# FMR FileVersions supported: 1, 2, 3, 4, 5
#
# Version:  v0.7a
# Build:    7082720
# Date:     Aug-27 2007, 8:17 PM CEST
# Author:   Jochen Weber, Brain Innovation, B.V., Maastricht, NL
# URL/Info: http://wiki.brainvoyager.com/BVQXtools

# FILE FORMAT
Description:Functional MRI files
Extensions:fmr
FieldDelimiters: {[32]}
LineDelimiters: {[13, 10], [10]}
ParagraphArrays:0
SkipEmptyLines:1
Magic:|
name          |range       |type    |magic
FMR_ldsamr    |1, 1024     |regexpi |loadamrfile\:\s*\w+\s*showamrfile\:\s*\d
EndMagic

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

# on read, check file version before attempt
EXPRE!$TFFREAD           !!!!!!@@ = BVQXfile(0, 'newcont', 'fmr'); if ~isempty(strfind(linecont{linec}, 'FileVersion')), @FileVersion = 2; else @FileVersion = 1; end
FIELD!@FileVersion > 1   !FileVersion            !double  !%d     !1      !4       !FileVersion
FLIST!                   !NrOfVolumes            !double  !%d     !1      !        !NrOfVolumes
FLIST!                   !NrOfSlices             !double  !%d     !1      !        !NrOfSlices

# FileVersion 1
BLOOP!@FileVersion == 1  !HasFV1                 !!!1 !!HasFV1
FLIST!                   !NrOfFirstVolume        !double  !%d     !1      !        !NrOfFirstVolume
FLIST!                   !NrOfFirstSlice         !double  !%d     !1      !        !NrOfFirstSlice
ELOOP!                   !HasFV1                 !!!  !!HasFV1

# FileVersion denoted
FIELD!@FileVersion > 1   !NrOfSkippedVolumes     !double  !%d     !1      !        !NrOfSkippedVolumes
FIELD!@FileVersion < 5   !Prefix                 !string  !%s     !1      !        !Prefix
FIELD!@FileVersion > 4   !Prefix                 !string  !"%s"   !1      !        !Prefix
FIELD!@FileVersion > 4   !DataStorageFormat      !double  !%d     !1      !2       !DataStorageFormat
EXPRE!$TFFREAD && @FileVersion < 5 !!!!!!@DataStorageFormat = 1;
FLIST!                   !TR                     !double  !%d     !1      !        !TR
FLIST!                   !InterSliceTime         !double  !%d     !1      !        !InterSliceTime
FLIST!@FileVersion > 1   !TimeResolutionVerified !double  !%d     !1      !        !TimeResolutionVerified
FIELD!@FileVersion > 4   !TE                     !double  !%d     !1      !        !TE
EXPRE!$TFFREAD && @FileVersion < 5 !!!!!!@TE = 30;
FIELD!@FileVersion > 3   !SliceAcquisitionOrder  !double  !%d     !1      !        !SliceAcquisitionOrder
FIELD!@FileVersion > 3   !SliceAcquisitionOrderVerified !double !%d !1    !        !SliceAcquisitionOrderVerified
EXPRE!$TFFREAD && @FileVersion < 4 !!!!!!@SliceAcquisitionOrder = []; @SliceAcquisitionOrderVerified = [];
FLIST!                   !ResolutionX            !double  !%d     !1      !        !ResolutionX
FLIST!                   !ResolutionY            !double  !%d     !1      !        !ResolutionY
FLIST!                   !LoadAMRFile            !string  !"%s"   !1      !        !LoadAMRFile
FLIST!                   !ShowAMRFile            !double  !%d     !1      !        !ShowAMRFile
FLIST!                   !ImageIndex             !double  !%d     !1      !        !ImageIndex
FLIST!                   !LayoutNColumns         !double  !%d     !1      !        !LayoutNColumns
FLIST!                   !LayoutNRows            !double  !%d     !1      !        !LayoutNRows
FLIST!                   !LayoutZoomLevel        !double  !%d     !1      !        !LayoutZoomLevel
FLIST!                   !SegmentSize            !double  !%d     !1      !        !SegmentSize
FLIST!                   !SegmentOffset          !double  !%d     !1      !        !SegmentOffset
FIELD!@FileVersion > 4   !NrOfLinkedProtocols    !double  !%d     !1      !1       !NrOfLinkedProtocols
EXPRE!$TFFREAD && @FileVersion < 5 !!!!!!@NrOfLinkedProtocols = 1;
FIELD!@FileVersion < 5   !ProtocolVersion        !double  !%d     !1      !2       !ProtocolVersion
EXPRE!$TFFREAD && @FileVersion > 4 !!!!!!@ProtocolVersion = 2;
FLIST!                   !ProtocolFile           !string  !"%s"   !1      !        !ProtocolFile

# Fields for FileVersion > 1
BLOOP!@FileVersion > 1   !HasFV2Plus             !!!1 !!HasFV2Plus
FLIST!                   !InplaneResolutionX     !double  !%f     !1      !        !InplaneResolutionX
FLIST!                   !InplaneResolutionY     !double  !%f     !1      !        !InplaneResolutionY
FLIST!                   !SliceThickness         !double  !%f     !1      !        !SliceThickness
FLIST!                   !SliceGap               !double  !%f     !1      !        !SliceGap
FLIST!                   !VoxelResolutionVerified!double  !%d     !1      !        !VoxelResolutionVerified
ELOOP!                   !HasFV2Plus             !!!  !!HasFV2Plus

# Fields for FileVersion > 2
BLOOP!@FileVersion > 2   !HasFV3Plus             !!!1 !!HasFV3Plus
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

# Either Convention or RadiologicalConvention
FLIST!@FileVersion < 4   !Convention             !double  !%d     !1      !        !Convention
FLIST!@FileVersion > 3   !RadiologicalConvention !string  !%s     !1      !YES     !RadiologicalConvention

# Two more empty lines
WRTLN!@FileVersion > 3   !!!!!!  # empty line
WRTLN!@FileVersion > 3   !!!!!!  # empty line
FIELD!@FileVersion > 3   !FirstDataSourceFile    !string  !"%s"   !1      !        !FirstDataSourceFile

# End of fields
ELOOP!                   !HasFV3Plus             !!!1 !!HasFV3Plus

# read STC if in new format
EXPRE!$TFFREAD      !!!!!!@Slice = []; dtsf = @DataStorageFormat; if any([1, 2] == dtsf), if dtsf == 1, tsnum = '1'; else, tsnum = ''; end, fmrf = fileparts($FILENAME); stcx = ''; if exist([fmrf '/' @Prefix tsnum '.stc'], 'file') == 2, stcx = '.stc'; else, if exist([fmrf '/' @Prefix tsnum '.STC'], 'file') == 2, stcx = '.STC'; end, end, if ~isempty(stcx), nov = @NrOfVolumes; nos = @NrOfSlices; rsx = @ResolutionX; rsy = @ResolutionY; stcsz = [rsx, rsy, nov, nos]; try, @Slice = struct; @Slice.STCData = []; switch(dtsf), case {1}, for tsc = 1:nos, stcf = sprintf('%s/%s%d%s', fmrf, @Prefix, tsc, stcx); @Slice(tsc).STCData = transio(stcf, 'ieee-le', 'uint16', 4, stcsz(1:3)); end, case {2}, @Slice.STCData = transio([fmrf '/' @Prefix stcx], 'ieee-le', 'uint16', 0, stcsz); end, catch, @Slice = []; warning('Error reading STC data.'); end, end, end
EXPRE!$TFFWRITE     !!!!!!if ~any([1, 2] == @DataStorageFormat), warning('Invalid DataStorageFormat.'); elseif ~isempty(@Slice) && isstruct(@Slice) && isfield(@Slice, 'STCData'), [fmrf{1:3}] = fileparts($FILENAME); if any(fmrf{3}(2:end) == upper(fmrf{3}(2:end))), stcx = '.STC'; else, stcx = '.stc'; end, stctf = [fmrf{1} '/' @Prefix]; nov = @NrOfVolumes; nos = @NrOfSlices; rsx = @ResolutionX; rsy = @ResolutionY; stcsz = [rsx, rsy, nov, nos]; try, switch (@DataStorageFormat), case {1}, for tsc = 1:nos, stcf = sprintf('%s%d%s', stctf, tsc, stcx); stcd = @Slice(tsc).STCData; if istransio(stcd), tios = struct(stcd); if ~strcmpi(tios.FileName, stcf), if ~cpfile(tios.FileName, stcf, 1); error('FILE_COPY_ERROR'); end, @Slice(tsc).STCData = transio(stcf, 'ieee-le', 'uint16', 4, tios.DataDims); end, else, stci = fopen(stcf, 'w', 'ieee-le'); if stci < 1, error('FILE_OPEN_ERROR'); end, fwrite(stci, stcsz(1:2), 'uint16'); fwrite(stci, @Slice(tsc).STCData(:), 'uint16'); fclose(stci); end, end, case{2}, stcf = [stctf stcx]; stcd = @Slice.STCData; if istransio(stcd), tios = struct(stcd); if ~strcmpi(tios.FileName, stcf), if ~cpfile(tios.FileName, stcf, 1); error('FILE_COPY_ERROR'); end, @Slice.STCData = transio(stcf, 'ieee-le', 'uint16', 0, tios.DataDims); end, else, stci = fopen(stcf, 'w', 'ieee-le'); if stci < 1, error('FILE_OPEN_ERROR'); end, fwrite(stci, @Slice.STCData(:), 'uint16'); fclose(stci); end, end, end, end

# end of fields

EndListOfFields

NewFileCode:!
@FileVersion = 5;
@NrOfVolumes = 0;
@NrOfSlices = 30;
@NrOfSkippedVolumes = 0;
@Prefix = 'untitled-';
@DataStorageFormat = 2;
@TR = 2000;
@InterSliceTime = @TR / @NrOfSlices;
@TimeResolutionVerified = 0;
@TE = 30;
@SliceAcquisitionOrder = 0;
@SliceAcquisitionOrderVerified = 0;
@ResolutionX = 64;
@ResolutionY = 64;
@LoadAMRFile = '';
@ShowAMRFile = 0;
@ImageIndex = 0;
@LayoutNColumns = 6;
@LayoutNRows = fix(0.99 + @NrOfSlices / @LayoutNColumns);
@LayoutZoomLevel = 1;
@SegmentSize = 10;
@SegmentOffset = 0;
@NrOfLinkedProtocols = 1;
@ProtocolVersion = 2;
@ProtocolFile = '<none>';
@InplaneResolutionX = 3;
@InplaneResolutionY = 3;
@SliceThickness = 3;
@SliceGap = 1;
@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>';
@Slice = [];
EndNewFileCode