文件列表:

._Notes (4096, 2012-04-06)
AIFViewer.m (4162, 2012-04-06)
AIFViewerSubsets.m (4618, 2012-04-06)
AIFViewer_multiSRTResult.m (6128, 2012-04-06)
AIFViewer_multiSRTSubsets.m (4616, 2012-04-06)
AutoSegment.m (24264, 2012-04-06)
Auto_all_ForDualBolus.m (3718, 2012-04-06)
Auto_all_Script.m (3535, 2012-04-06)
Auto_all_Script_subsets.m (460, 2012-04-06)
Best_Segmentation.m (4589, 2012-04-06)
CR_editor.fig (17288, 2012-04-06)
CR_editor.m (67635, 2012-04-06)
CR_editor.m(non-global) (55773, 2012-04-06)
CheckLength.m (2018, 2012-04-06)
ConstructAndProcessSubsets.m (7326, 2012-04-06)
Cpg.m (563, 2012-04-06)
Cps.m (904, 2012-04-06)
Documentation.odt (18057, 2012-04-06)
Documentation.pdf (72912, 2012-04-06)
EnsureConectivity.m (1553, 2012-04-06)
ExtractCurve_STDs.m (3892, 2012-04-06)
ExtractCurves.m (3878, 2012-04-06)
ExtractCurves_useWith_CReditor.m (3876, 2012-04-06)
FindBigest.m (635, 2012-04-06)
FindLVRV.m (3815, 2012-04-06)
FindSomething.m (1125, 2012-04-06)
Fixer.fig (19399, 2012-04-06)
Fixer.m (24091, 2012-04-06)
GaneshModel.m (2384, 2012-04-06)
ImgOverlays_P082609.m (3979, 2012-04-06)
InterpTimeCurve2.m (1504, 2012-04-06)
NcutComputeW.m (5421, 2012-04-06)
NcutImageSegment.m (3115, 2012-04-06)
NcutPartition.m (3547, 2012-04-06)
NcutValue.m (1384, 2012-04-06)
NeighboringTemporalSmoothingRegistration.m (3510, 2012-04-06)
Notes (9073, 2012-04-06)
ProcessDataFiles.m (1774, 2012-04-06)
ReadPar.m (736, 2012-04-06)
... ...

%function kSpace = readMeasDataVB15(filename) % Program to read measurement data from Siemens MRI scanners % with IDEA VB15 using Matlab 7 (single value) % % function [kSpace] = readMeasDataVB15(filename) % If input argument 'filename' is not defined % use GUI to select file with measurements (*.dat) % kSpace - measured k-space data % % Version 1.0 % AUTHOR of MATLAB implementation: Eugene G. Kholmovski, PhD % UCAIR, Department of Radiology, University of Utah % ekhoumov@ucair.med.utah.edu %% GUI to define filename for measurement file %if nargin == 0 filename = ''; if length(filename) == 0 [temp path] = uigetfile('*.dat','Select File to Read'); filename = [path temp(1:length(temp)-4)]; nargin = 0; end %end %% Definition of OFF and ON constants OFF = 0; ON = 1; %% resetFFTscale should be equal to 1 to reset FFTscale and DataCorrection %% for each coil to 1 resetFFTscale = OFF; %% Flags to Read Meas Data from Individual Coil readOneCoil = OFF; % coilIndex defines which coil element data will be read % when readOneCoil = ON coilIndex = 1; %% Flags to remove oversampling (OS) in x-direction %% One of these flags should be equal to 1 to remove OS. %% removeOS=1 is more efficient as it processes each readout line %% independently reducing the required memory space to keep all measured %% data. removeOS = OFF; % EVRD 8/27/08, just to try with radial and compare. Not good! Back to OFF removeOSafter = OFF; % note this works in image space, cutting FOV. Not likely good idea for radial %% transformToImageSpace should be equal to 1 to get image space %% representation. Take into account that no correction for partial Fourier %% or parallel imaging k-space undersampling is done. %% The given version of code only uses FFT operation. transformToImageSpace = OFF; %% Flags readPhaseCorInfo = OFF; readNavigator = OFF; readTimeStamp = ON; %% writeToFile should be equal to 1 to save k-space or image space volume in Matlab file (*.mat) writeToFile = ON; if writeToFile == 1 if transformToImageSpace == 0 filenameOut = sprintf('%s_Kspace',filename); else filenameOut = sprintf('%s_imageSpace',filename); end end %% Useful Parameters globalHeader = 32; localHeader = 128; %% Read Protocol from filename.dat file if nargin == 1 fid = fopen(filename,'r','ieee-le'); else fid = fopen([filename '.dat'],'r','ieee-le'); end dataField = fread(fid,1,'int32'); info = fread(fid,dataField-4,'uchar'); info = char(info'); fclose(fid); longProtocol = info; textStart = 'MeasYaps'; textEnd = 'Phoenix'; indexStart = strfind(info,textStart) + length(textStart) + 5; indexEnd = strfind(info,textEnd) - 3; shortProtocol = info(indexStart:indexEnd); clear info; info = shortProtocol; %% Some Acquisition Parameters from filename.asc text = 'ucDimension = 0x'; t = strfind(info,text) + length(text); ScanDimension = sscanf(info(t:t+10),'%d'); if ScanDimension == 4 flag3D = ON; else flag3D = OFF; end text = 'sKSpace.lBaseResolution = '; t = strfind(info,text) + length(text); NxAll = sscanf(info(t:t+10),'%d'); text = 'sKSpace.lPhaseEncodingLines = '; t = strfind(info,text) + length(text); NyAll = sscanf(info(t:t+10),'%d'); text = 'sKSpace.dPhaseOversamplingForDialog = '; t = strfind(info,text) + length(text); if isempty(t) == 1 OSfactorPE = 1; else OSfactorPE = 1 + sscanf(info(t:t+10),'%f'); end text = 'sKSpace.lPartitions = '; t = strfind(info,text) + length(text); NzAll = sscanf(info(t:t+10),'%d'); text = 'sKSpace.dSliceOversamplingForDialog = '; t = strfind(info,text) + length(text); if isempty(t) == 1 OSfactor3D = 1; else OSfactor3D = 1 + sscanf(info(t:t+10),'%f'); end text = 'sKSpace.dPhaseResolution = '; t = strfind(info,text) + length(text); phaseResolution = sscanf(info(t:t+10),'%f'); text = 'sKSpace.dSliceResolution = '; t = strfind(info,text) + length(text); sliceResolution = sscanf(info(t:t+10),'%f'); text = 'sSliceArray.lSize = '; t = strfind(info,text) + length(text); Nsl = sscanf(info(t:t+10),'%d'); text = 'sSliceArray.lConc = '; t = strfind(info,text) + length(text); Nconc = sscanf(info(t:t+10),'%d'); text = '.lRxChannelConnected = '; t = strfind(info,text) + length(text); Nc = length(t); text = 'AdjustSeq%/AdjCoilSensSeq'; t = strfind(info,text) + length(text); if isempty(t) == 0 Nc = Nc-1; end text = 'lContrasts = '; t = strfind(info,text) + length(text); if isempty(t) == 1 nContrast = 1; else nContrast = sscanf(info(t:t+10),'%d'); end text = 'lSets = '; t = strfind(info,text) + length(text); if isempty(t) == 1 nSet = 1; else nSet = sscanf(info(t:t+10),'%d'); end text = 'lAverages = '; t = strfind(info,text) + length(text); if isempty(t) == 1 nAverage = 1; else nAverage = sscanf(info(t:t+10),'%d'); end text = 'lRepetitions = '; t = strfind(info,text) + length(text); if isempty(t) == 1 nRepetition = 1; else nRepetition = sscanf(info(t:t+10),'%d') + 1; end text = 'sPhysioImaging.lPhases = '; t = strfind(info,text) + length(text); if isempty(t) == 1 nPhase = 1; else nPhase = sscanf(info(t:t+10),'%d'); end text = 'sKSpace.PhasePartialFourier = 0x'; t = strfind(info,text) + length(text); if isempty(t) == 1 fractionFlag = 10; else fractionFlag = str2num(info(t:t+1)); end switch(fractionFlag) case(10) fractionY = 1.0; case(8) fractionY = 7/8; case(4) fractionY = 0.75; case(2) fractionY = 5/8; case(1) fractionY = 0.5; end text = 'sKSpace.SlicePartialFourier = 0x'; t = strfind(info,text) + length(text); if isempty(t) == 1 fractionFlag = 10; else fractionFlag = str2num(info(t:t+1)); end switch(fractionFlag) case(10) fractionZ = 1.0; case(8) fractionZ = 7/8; case(4) fractionZ = 0.75; case(2) fractionZ = 5/8; case(1) fractionZ = 0.5; end text = 'sKSpace.dSeqPhasePartialFourierForSNR = '; t = strfind(info,text) + length(text); if isempty(t) == 1 phasePartialFourierForSNR = 1.0; else phasePartialFourierForSNR = sscanf(info(t:t+10),'%f'); end text = 'sFastImaging.lEPIFactor = '; t = strfind(info,text) + length(text); EPIFactor = sscanf(info(t:t+10),'%d'); text = 'sFastImaging.lTurboFactor = '; t = strfind(info,text) + length(text); if isempty(t) == 1 turboFactor = 1; else turboFactor = sscanf(info(t:t+10),'%d'); end %% iPAT parameters from filename.asc text = 'sPat.ucPATMode = 0x'; t = strfind(info,text) + length(text); PATMode = str2num(info(t:t+1)); text = 'sPat.ucRefScanMode = 0x'; t = strfind(info,text) + length(text); PATRefScanMode = str2num(info(t:t+1)); text = 'sPat.lAccelFactPE = '; t = strfind(info,text) + length(text); AccelFactorPE = sscanf(info(t:t+10),'%d'); text = 'sPat.lAccelFact3D = '; t = strfind(info,text) + length(text); AccelFactor3D = sscanf(info(t:t+10),'%d'); if AccelFactorPE == 1 nRefLinesPE = 0; else text = 'sPat.lRefLinesPE = '; t = strfind(info,text) + length(text); nRefLinesPE = sscanf(info(t:t+10),'%d'); end if AccelFactor3D == 1 nRefLines3D = 0; else text = 'sPat.lRefLines3D = '; t = strfind(info,text) + length(text); nRefLines3D = sscanf(info(t:t+10),'%d'); end clear info; info = longProtocol; text = 'ParamLong."iMaxNoOfRxChannels'; t = strfind(info,text) + length(text); if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); Nct = str2num(ss(isstrprop(ss,'digit'))); if Nct < Nc Nc = Nct; end end text = 'ParamLong."lNoOfPhaseCorrScans'; t = strfind(info,text) + length(text); if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 nPhCorrScan = str2num(ss(isstrprop(ss,'digit'))); end end if turboFactor > 1 nPhCorEcho = 1; nPhCorScan = 1; end if EPIFactor > 1 nPhCorScan = 1; nPhCorEcho = 3; end if AccelFactorPE == 1 FirstFourierLine = 1; FirstRefLine = 1; else text = 'ParamLong."lFirstFourierLine'; t = strfind(info,text) + length(text); FirstFourierLine = 0; if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 FirstFourierLine = str2num(ss(isstrprop(ss,'digit'))); end end FirstFourierLine = FirstFourierLine + 1; text = 'ParamLong."lFirstRefLine'; t = strfind(info,text) + length(text); FirstRefLine = 0; if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 FirstRefLine = str2num(ss(isstrprop(ss,'digit'))); end end FirstRefLine = FirstRefLine + 1; end if AccelFactor3D == 1 FirstFourierPar = 1; FirstRefPartition = 1; else text = 'ParamLong."lFirstFourierPartition'; t = strfind(info,text) + length(text); FirstFourierPartition = 0; if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 FirstFourierPartition = str2num(ss(isstrprop(ss,'digit'))); end end FirstFourierPartition = FirstFourierPartition + 1; text = 'ParamLong."lFirstRefPartition'; FirstRefPartition = 0; t = strfind(info,text) + length(text); if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 FirstRefPartition = str2num(ss(isstrprop(ss,'digit'))); if FirstRefPartition < 0 FirstRefPartition = 0; end end end FirstRefPartition = FirstRefPartition + 1; end %% YAPS Parameters from filename.asc text = 'iNoOfFourierColumns'; t = strfind(info,text) + length(text); ss = sscanf(info(t:t+35),'%s'); NxOS = str2num(ss(isstrprop(ss,'digit'))); text = 'flReadoutOSFactor'; t = strfind(info,text) + length(text); OSfactorRO = sscanf(info(t:t+10),'%f'); OSfactorRO = 2; Nx = round(NxOS/OSfactorRO); text = 'NoOfFourierLines'; t = strfind(info,text) + length(text); ss = sscanf(info(t:t+35),'%s'); Ny = str2num(ss(isstrprop(ss,'digit'))); text = 'iNoOfFourierPartitions'; t = strfind(info,text) + length(text); ss = sscanf(info(t:t+35),'%s'); Nz = str2num(ss(isstrprop(ss,'digit'))); text = 'iRoFTLength'; t = strfind(info,text) + length(text); ss = sscanf(info(t:t+35),'%s'); NxRecon = str2num(ss(isstrprop(ss,'digit'))); text = 'iPEFTLength'; t = strfind(info,text) + length(text); ss = sscanf(info(t:t+35),'%s'); NyRecon = str2num(ss(isstrprop(ss,'digit'))); text = 'i3DFTLength'; t = strfind(info,text) + length(text); ss = sscanf(info(t:t+35),'%s'); NzRecon = str2num(ss(isstrprop(ss,'digit'))); if Nz == 1 NzRecon = 1; end text = 'ParamLong."ushSlicePerConcat'; t = strfind(info,text) + length(text); ss = sscanf(info(t:t+35),'%s'); NslicePerConcat = str2num(ss(isstrprop(ss,'digit'))); %% Partial Fourier Mode and Parameters from filename.asc text = 'lPCAlgorithm'; t = strfind(info,text) + length(text); ss = sscanf(info(t:t+35),'%s'); PCAlgorithm = str2num(ss(isstrprop(ss,'digit'))); text = 'ParamLong."lNoOfPhaseCorrColumns'; t = strfind(info,text) + length(text); NoOfPhaseCorrColumns = Nx/2; if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 NoOfPhaseCorrColumns = str2num(ss(isstrprop(ss,'digit'))); end end text = 'ParamLong."lNoOfPhaseCorrLines'; t = strfind(info,text) + length(text); NoOfPhaseCorrLines = NyAll/2; if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 NoOfPhaseCorrLines = str2num(ss(isstrprop(ss,'digit'))); end end text = 'ParamLong."lNoOfPhaseCorrPartitions'; t = strfind(info,text) + length(text); NoOfPhaseCorrPartitions = NzAll/2; if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 NoOfPhaseCorrPartitions = str2num(ss(isstrprop(ss,'digit'))); end end text = 'ParamLong."lColSlopeLength'; t = strfind(info,text) + length(text); ColSlopeLength = Nx/4; if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 ColSlopeLength = str2num(ss(isstrprop(ss,'digit'))); end end text = 'ParamLong."lLinSlopeLength'; t = strfind(info,text) + length(text); ColSlopeLength = NyAll/4; if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 LinSlopeLength = str2num(ss(isstrprop(ss,'digit'))); end end text = 'ParamLong."lParSlopeLength'; t = strfind(info,text) + length(text); ParSlopeLength = NzAll/4; if isempty(t) == 0 ss = sscanf(info(t:t+35),'%s'); if isempty(str2num(ss(isstrprop(ss,'digit')))) == 0 ParSlopeLength = str2num(ss(isstrprop(ss,'digit'))); end end clear info; info = shortProtocol; %% Raw Data Correction Factors CorrFactor = ones(Nc,1); if ON == 0 for c=1:Nc text = 'axRawDataCorrectionFactor[0]['; text = sprintf('%s%d',text,c-1); if c < 11 text = [text,'].dRe =']; else text = [text,'].dRe =']; end t = strfind(info,text) + length(text); if isempty(t) == 1 CorrFactor(c) = 1; else CorrFactor(c) = sscanf(info(t:t+20),'%f'); end text = 'axRawDataCorrectionFactor[0]['; text = sprintf('%s%d',text,c-1); if c < 11 text = [text,'].dIm =']; else text = [text,'].dIm =']; end t = strfind(info,text) + length(text); if isempty(t) == 0 CorrFactor(c) = CorrFactor(c) + i*sscanf(info(t:t+20),'%f'); end end end %% FFT Correction Factors FFTCorrFactor = ones(Nc,1); for c=1:Nc text = 'aFFT_SCALE['; text = sprintf('%s%d',text,c-1); if c < 11 text = [text,'].flFactor = ']; else text = [text,'].flFactor = ']; end % text = [text,'].flFactor']; % evrd 4/08 to read brain 12 coil t = strfind(info,text) + length(text); % t=t+3; % evrd to get back the space = space % keyboard FFTCorrFactor(c) = sscanf(info(t:t+20),'%f'); % FFTCorrFactor(c) = sscanf(info(t+10:t+18),'%f'); end if resetFFTscale == 1 FFTCorrFactor = ones(Nc,1); end %% For PC Angio Nset = 1; text = 'sAngio.ucPCFlowMode = 0x'; t = strfind(info,text) + length(text); if isempty(t) == 0 PCMRAFlag = sscanf(info(t:t+1),'%d'); else PCMRAFlag = 0; end if PCMRAFlag == 1 text = 'sAngio.sFlowArray.lSize = '; t = strfind(info,text) + length(text); if isempty(t) == 0 Nset = sscanf(info(t:t+2),'%d') + 1; end end clear info; %% Recalculation of partial Fourier factors and EPI/turbo factor for EPI and TSE fractionPE = Ny/NyAll; fraction3D = Nz/NzAll; EPIFactor = round(fractionPE*EPIFactor); nEPITrain = Ny/EPIFactor; turboFactor = round(fractionPE*turboFactor); nTSETrain = Ny/turboFactor; Nc0 = Nc; if readOneCoil == 1 Nc = 1; else Nc = Nc0; end %% Calculation of the number of valid k-space readouts and k-space data matrix dimensions if PATMode == 1 nReadout = nAverage*nPhase*nRepetition*nContrast*Nsl*Nz*Nc*Ny; elseif PATMode == 2 & PATRefScanMode == 2 if mod(Ny,2) == 1 NyPAT = (Ny-1+nRefLinesPE*(AccelFactorPE-1))/AccelFactorPE; else NyPAT = floor((Ny+nRefLinesPE*(AccelFactorPE-1))/AccelFactorPE); end nReadout = nAverage*nPhase*nRepetition*nContrast*Nsl*Nz*Nc*NyPAT; end if removeOS == 1 kSpace = zeros(nAverage, nPhase, nRepetition, nContrast, Nsl, Nc, Nz, Nx, Ny, 'single'); else kSpace = zeros(nAverage, nPhase, nRepetition, nContrast, Nsl, Nc, Nz, NxOS, Ny, 'single'); end if readPhaseCorInfo == 1 & nPhCorScan > 0 kPhaseCor = zeros(nPhCorScan, nPhCorEcho, Nsl, nRepetition, Nc, NxOS, 'single'); end if readNavigator == 1 nNavigator = nAverage*nPhase*nRepetition*nContrast*Nsl*Nz*Nc*nEPITrain*nNavEK; kNavigator = zeros(nAverage, nPhase, nRepetition, nContrast*nNavEK, Nsl, Nc, Nz, nEPITrain, NxOS, 'single'); end if readTimeStamp == 1 nTimeStamp = nAverage*nPhase*nRepetition*nContrast*Nz; timeStamp = zeros(nAverage, nPhase, nRepetition, nContrast*nNavEK, Nz, 'single'); end %keyboard; %%% DATA READOUT & REORDERING %% Read k-space data from filename.dat noiseMeasCounter = 0; noiseMeas = zeros(NxOS,Nc); navigatorPrep = 0; LineN = -1; Ndr = 1; for r=1:Ndr xCoil = r-1 if nargin == 1 fid = fopen(filename,'r','ieee-le'); else fid = fopen([filename '.dat'],'r','ieee-le'); end readFlag = 1; skipField = 0; count = 0; countNavigator = 0; navigatorDataON = 0; temp1 = zeros(NxOS,1); dataField = fread(fid,1,'int32'); st = fseek(fid,dataField,-1); while (readFlag == 1) if readTimeStamp == 1 st = fseek(fid,12,0); timeS = fread(fid,1,'uint32'); st = fseek(fid,4,0); else st = fseek(fid,20,0); end evalMask1 = fread(fid,1,'uint32'); evalMask2 = fread(fid,1,'uint32'); flag = 33-find(dec2base(evalMask1,2,32) == '1'); Nxr = fread(fid,1,'uint16'); Ncr = fread(fid,1,'uint16'); Line = fread(fid,1,'uint16'); Acquisition = fread(fid,1,'uint16'); Slice = fread(fid,1,'uint16'); Partition = fread(fid,1,'uint16'); Echo = fread(fid,1,'uint16'); Phase = fread(fid,1,'uint16'); Repetition = fread(fid,1,'uint16'); Set = fread(fid,1,'uint16'); st = fseek(fid,12,0); CutOffDataPre = fread(fid,1,'uint16'); CutOffDataPost = fread(fid,1,'uint16'); KSpaceCentreColumn = fread(fid,1,'uint16'); CoilMode = fread(fid,1,'uint16'); ReadOutOffCentre = fread(fid,1,'float32'); st = fseek(fid,4,0); KSpaceCentreLineNo = fread(fid,1,'uint16'); KSpaceCentrePartitionNo = fread(fid,1,'uint16'); st = fseek(fid,44,0); Channel = fread(fid,1,'uint16'); st = fseek(fid,2,0); if isempty(find(flag == 1)) == 0 break; end if isempty(find(flag == 2)) == 0 | isempty(find(flag == 22)) == 0 | isempty(find(flag == 26)) == 0 if isempty(find(flag == 22)) == 0 & readPhaseCorInfo == 0 skipField = nPhCorScan*nPhCorEcho*Ncr*(localHeader+8*Nxr)-localHeader; end if isempty(find(flag == 22)) == 0 & readPhaseCorInfo == 1 skipField = -localHeader; st = fseek(fid,skipField,0); skipField = 0; for m = 1:nPhCorScan*nPhCorEcho*Ncr infoMDH_TimeStamp = readMDH_TimeStamp_VB13(fid); temp = fread(fid,2*Nxr,'float32'); ... ...

近期下载者：

相关文件：

评论：[我要评论] [举报此文件]

收藏者：