Changeset 154


Ignore:
Timestamp:
Jan 21, 2011, 1:29:53 PM (8 years ago)
Author:
tjniskan
Message:
  • Fixed a few bugs in aedes_readvnmr.m. The new VNMR read function should work with most data now.

M aedes_readvnmr.m
M aedes_revision.m

Files:
2 edited

Legend:

Unmodified
Added
Removed
  • aedes_readvnmr.m

    r153 r154  
    9797%                                               % AEDES_READPROCPAR
    9898%
     99%        'SortPSS'     :  [ 'off' | {'on'} ]    % Sort slices in 2D stacks
     100%                                               % using pss. Turn this 'off'
     101%                                               % if interleaved slice
     102%                                               % order is to be preserved.
     103%                                               % The original pss is saved
     104%                                               % in procpar.pss_orig
     105%
    99106%        'ZeroPadding' :  ['off'|'on'|{'auto'}] % 'off' = force
    100107%                                               % zeropadding off
     
    217224Dat.ReorientEPI = false;
    218225Dat.RemoveEPIphaseIm = true;
    219 Dat.EPIBlockSize = 100;
     226Dat.EPIBlockSize = 300;
    220227Dat.EPIPhasedArrayData = false;
    221228Dat.OrientImages = true;
    222229Dat.SumOfSquares = 1;
    223230Dat.UseCustomRecon = true;
     231Dat.SortPSS = true;
    224232
    225233% Default custom reconstruction file directory
     
    680688  else
    681689    % Use the default reconstruction code
    682     [kspace,msg_out]=l_ReconstructKspace(kspace,Dat,procpar);
    683    
     690    [kspace,msg_out,procpar]=l_ReconstructKspace(kspace,Dat,procpar);
     691    DATA.PROCPAR = procpar;
     692               
    684693    % Fourier transform data
    685694    if Dat.ReturnFTData
     
    10721081% Reconstruct k-space
    10731082% ==================================================================
    1074 function [kspace,msg_out]=l_ReconstructKspace(kspace,Dat,procpar)
     1083function [kspace,msg_out,procpar]=l_ReconstructKspace(kspace,Dat,procpar)
    10751084
    10761085msg_out = '';
     
    11551164  % Reconstruct 2D data
    11561165  if strcmpi(seqcon,'ncsnn')
    1157     kspace = reshape(kspace,[np/2,etl,ns,ArrayLength,nv/etl,nRcvrs]);
    1158     kspace = permute(kspace,[1 2 5 3 4 6]);
     1166    kspace = reshape(kspace,[np/2,etl,ns,nRcvrs,ArrayLength,nv/etl]);
     1167    kspace = permute(kspace,[1 2 6 3 5 4]);
    11591168    kspace = reshape(kspace,[np/2,nv,ns*ArrayLength,1,nRcvrs]);
    11601169  elseif strcmpi(seqcon,'nscnn')
    11611170    if isfield(procpar,'flash_converted')
    1162       kspace = reshape(kspace,[np/2,nRcvrs,ArrayLength,nv,ns]);
    1163       kspace = permute(kspace,[1 4 5 3 2]);
     1171      kspace = reshape(kspace,[np/2,nRcvrs,ArrayLength,ns,nv]);
     1172      kspace = permute(kspace,[1 5 4 3 2]);
    11641173      kspace = reshape(kspace,[np/2,nv,ns*ArrayLength,1,nRcvrs]);
    11651174    else
     
    11911200end
    11921201
    1193 
     1202% Sort interleaved 2D data using pss
     1203[sorted_pss,I_pss]=sort(procpar.pss);
     1204if ~ismember(procpar.pss,sorted_pss,'rows') && Dat.SortPSS
     1205        kspace = kspace(:,:,I_pss,:,:);
     1206        procpar.pss_orig = procpar.pss;
     1207        procpar.pss = sorted_pss;
     1208end
    11941209
    11951210% ==================================================================
  • aedes_revision.m

    r153 r154  
    9393% bash-script every time it is called so that this file "aedes_revision.m" is
    9494% always in the list of committed files. DO NOT EDIT THE NEXT LINE!!!
    95 % - SVN Hook -
     95% - Svn Hook -
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