Skip to content

Commit

Permalink
support UIH dicom
Browse files Browse the repository at this point in the history
  • Loading branch information
@xiangruili
xiangruili committed Sep 16, 2018
1 parent ae1d301 commit 47ad9e6
Show file tree
Hide file tree
Showing 2 changed files with 104 additions and 18 deletions.
79 changes: 61 additions & 18 deletions dicm2nii.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -381,6 +381,7 @@
% 180614 Implement scale_16bit: free precision for tools using 16-bit datatype.
% 180619 use GetFullPath from Jan: (thx JulienB).
% 180721 accept mixture of files and folders as input; GUI uses jFileChooser().
% 180914 support UIH dicm, both GRID (mosaic) and regular.

% TODO: need testing files to figure out following parameters:
% flag for MOCO series for GE/Philips
Expand Down Expand Up @@ -943,6 +944,8 @@
end
elseif strncmpi(s.Manufacturer, 'Philips', 7)
tf = strcmp(tryGetField(s, 'MRSeriesDiffusion', 'N'), 'Y');
elseif strncmpi(s.Manufacturer, 'UIH', 3)
tf = isfield(s, 'B_value');
else % Some Siemens DTI are not labeled as \DIFFUSION
tf = ~isempty(csa_header(s, 'B_value'));
end
Expand Down Expand Up @@ -1339,6 +1342,24 @@
% t = (t - min(t)) * 24 * 3600 * 1000; % day to ms
% end

if isempty(t) && strncmpi(s.Manufacturer, 'UIH', 3)
t = zeros(nSL, 1);
if isfield(s, 'MRVFrameSequence') % mosaic
for j = 1:nSL
item = sprintf('Item_%g', j);
str = s.MRVFrameSequence.(item).AcquisitionDateTime;
t(j) = datenum(str, 'yyyymmddHHMMSS.fff');
end
else
dict = dicm_dict('', 'AcquisitionDateTime');
for j = 1:nSL
s1 = dicm_hdr(h{j}.Filename, dict);
t(j) = datenum(s1.AcquisitionDateTime, 'yyyymmddHHMMSS.fff');
end
end
t = (t - min(t)) * 24 * 3600 * 1000; % day to ms
end

if isempty(t) % non-mosaic Siemens: create 't' based on ucMode
ucMode = asc_header(s, 'sSliceArray.ucMode'); % 1/2/4: Asc/Desc/Inter
if isempty(ucMode), return; end
Expand Down Expand Up @@ -1414,8 +1435,7 @@
s2 = h{iDir(j)};
val = tryGetField(s2, 'B_value');
if val == 0, continue; end
vec = tryGetField(s2, 'DiffusionGradientDirection'); % Siemens/Philips
imgRef = isempty(vec); % likely GE if true. B_value=0 won't reach here
vec = tryGetField(s2, 'DiffusionGradientDirection'); % Siemens/Philips/UIH
if isempty(val) || isempty(vec) % likely GE
s2 = dicm_hdr(s2.Filename, dict);
end
Expand Down Expand Up @@ -1459,9 +1479,9 @@

% http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
[ixyz, R] = xform_mat(s, nii.hdr.dim(2:4)); % R takes care of slice dir
if exist('imgRef', 'var') && imgRef % GE bvec already in image reference
if strncmpi(s.Manufacturer, 'GE', 2) % GE bvec already in image reference
if strcmp(tryGetField(s, 'InPlanePhaseEncodingDirection'), 'ROW')
bvec = bvec(:, [2 1 3]);
bvec = bvec(:, [2 1 3]); % dicom bvec in Freq/Phase/Slice order
bvec(:, 2) = -bvec(:, 2); % because of transpose?
if ixyz(3)<3
errorLog(sprintf(['%s: bvec sign for non-axial acquisition with' ...
Expand Down Expand Up @@ -1568,7 +1588,7 @@ function save_dti_para(s, fname)
% rest are former: R = verify_slice_dir(R, s, dim, iSL)
if dim(3)<2, return; end % don't care direction for single slice

if s.Columns > dim(1) % Siemens mosaic: use dim(1) since no transpose to img
if s.Columns>dim(1) && strncmpi(s.Manufacturer, 'SIEMENS', 7) % Siemens mosaic
R(:,4) = R * [ceil(sqrt(dim(3))-1)*dim(1:2)/2 0 1]'; % real slice location
vec = csa_header(s, 'SliceNormalVector'); % mosaic has this
if ~isempty(vec) % exist for all tested data
Expand Down Expand Up @@ -1930,19 +1950,32 @@ function gui_callback(h, evt, cmd, fh)

if isfield(s, 'CSAImageHeaderInfo') % SIEMENS
phPos = csa_header(s, 'PhaseEncodingDirectionPositive'); % image ref
elseif isfield(s, 'ProtocolDataBlock') %GE
% elseif isfield(s, 'UserDefineData') % GE
% % https://github.com/rordenlab/dcm2niix/issues/163
% b = s.UserDefineData;
% i = typecast(b(25:26), 'uint16'); % hdr_offset
% v = typecast(b(i+1:i+4), 'single'); % 5.0 to 40.0
% if v >= 26, i = i + 76; end
% phPos = bitget(b(i+49), 3) > 0;
try % VIEWORDER "1" == bottom_up
phPos = s.ProtocolDataBlock.VIEWORDER == '1';
end
elseif isfield(s, 'Stack') %Philips
try d = s.Stack.Item_1.MRStackPreparationDirection(1); catch, return; end
% elseif isfield(s, 'ProtocolDataBlock') % GE
% try % VIEWORDER "1" == bottom_up
% phPos = s.ProtocolDataBlock.VIEWORDER == '1';
% end
elseif isfield(s, 'UserDefineData') % GE
% https://github.com/rordenlab/dcm2niix/issues/163
b = s.UserDefineData;
i = typecast(b(25:26), 'uint16'); % hdr_offset
flag2_off = 917;
v = typecast(b(i+1:i+4), 'single'); % 5.0 to 40.0
if v >= 25.002
flag2_off = flag2_off - 140;
i = i + 76;
end
% isEPI = bitget(b(i+59), 7) > 0;
flag1 = bitget(b(i+49), 3) > 0;
flag2 = b(i+flag2_off);
if flag2 == 2, phPos = ~flag1; end % BOTTOM_UP or TOP_DOWN
else
if isfield(s, 'Stack') % Philips
try d = s.Stack.Item_1.MRStackPreparationDirection(1); catch, return; end
elseif isfield(s, 'PEDirectionDisplayed') % UIH
try d = s.PEDirectionDisplayed(1); catch, return; end
else % unknown Manufacturer
return;
end
try R = reshape(s.ImageOrientationPatient, 3, 2); catch, return; end
[~, ixy] = max(abs(R)); % like [1 2]
if isempty(iPhase) % if no InPlanePhaseEncodingDirection
Expand All @@ -1958,6 +1991,15 @@ function gui_callback(h, evt, cmd, fh)

%% subfunction: extract useful fields for multiframe dicom
function s = multiFrameFields(s)
if isfield(s, 'MRVFrameSequence') % not real multi-frame dicom
try
s.ImagePositionPatient = s.MRVFrameSequence.Item_1.ImagePositionPatient;
s.AcquisitionDateTime = s.MRVFrameSequence.Item_1.AcquisitionDateTime;
item = sprintf('Item_%g', s.LocationsInAcquisition);
s.LastFile.ImagePositionPatient = s.MRVFrameSequence.(item).ImagePositionPatient;
end
return;
end
pffgs = 'PerFrameFunctionalGroupsSequence';
sfgs = 'SharedFunctionalGroupsSequence';
if any(~isfield(s, {sfgs pffgs})), return; end
Expand Down Expand Up @@ -2550,6 +2592,7 @@ function checkUpdate(mfile)
function nMos = nMosaic(s)
nMos = csa_header(s, 'NumberOfImagesInMosaic'); % healthy mosaic dicom
if ~isempty(nMos), return; end % seen 0 for GLM Design file and others
if isType(s, '\VFRAME'), nMos = s.LocationsInAcquisition; return; end % UIH

% The next fix detects mosaic which is not labeled as MOSAIC in ImageType, nor
% NumberOfImagesInMosaic exists, seen in syngo MR 2004A 4VA25A phase image.
Expand Down
43 changes: 43 additions & 0 deletions dicm_dict.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@
% 160411 dict contains group and element.
% 171211 Add Siemens grp 0021 and more.
% 180514 Guess more Siemens grp 0021 tags, correct BandwidthPerPixelPhaseEncode.
% 180914 Add vendor UIH.

if nargin<1, vendor = 'SIEMENS'; end
dict.vendor = vendor;
Expand Down Expand Up @@ -1208,7 +1209,49 @@
'2005' '1585' 'DS' 'PIIM_GRADIENT_SLEW_RATE'
'2005' '1587' 'DS' 'PIIM_MR_STUDY_B1RMS'
'2050' '0020' 'CS' 'PresentationLUTShape' }];
elseif strncmpi(vendor, 'UIH', 3)
C = [C; {
'0061' '1002' 'US' 'GeneratePrivate'
'0061' '4002' 'SH' 'FOV'
'0065' '1000' 'UL' 'MeasurmentUID'
'0065' '1002' 'SH' 'ImageOrientationDisplayed'
'0065' '1003' 'LO' 'ReceiveCoil'
'0065' '1004' 'SH' 'Interpolation'
'0065' '1005' 'SH' 'PEDirectionDisplayed'
'0065' '1006' 'IS' 'SliceGroupID'
'0065' '1007' 'OB' 'Uprotocol'
'0065' '1009' 'FD' 'B_value' % 'BActualValue'
'0065' '100A' 'FD' 'BUserValue'
'0065' '100B' 'DS' 'BlockSize'
'0065' '100C' 'SH' 'ExperimentalStatus'
'0065' '100D' 'SH' 'ParallelInformation'
'0065' '100F' 'SH' 'SlicePosition'
'0065' '1011' 'SH' 'Sections'
'0065' '1013' 'FD' 'InPlaneRotAngle'
'0065' '1014' 'DS' 'SliceNormalVector'
'0065' '1015' 'DS' 'SliceCenterPosition'
'0065' '1016' 'UL' 'PixelRotateModel'
'0065' '1017' 'LO' 'SARModel'
'0065' '1018' 'LO' 'dBdtModel'
'0065' '1023' 'LO' 'TablePosition'
'0065' '1025' 'DS' 'SliceGap'
'0065' '1029' 'SH' 'AcquisitionDuration'
'0065' '102B' 'LT' 'ApplicationCategory'
'0065' '102C' 'IS' 'RepeatitionIndex'
'0065' '102D' 'ST' 'SequenceDisplayName'
'0065' '102E' 'LO' 'NoiseDecovarFlag'
'0065' '102F' 'FL' 'ScaleFactor'
'0065' '1031' 'SH' 'MRSequenceVariant'
'0065' '1032' 'SH' 'MRKSpaceFilter'
'0065' '1033' 'SH' 'MRTableMode'
'0065' '1036' 'OB' 'MRDiscoParameter'
'0065' '1037' 'FD' 'DiffusionGradientDirection' % 'MRDiffusionGradOrientation'
'0065' '1038' 'FD' 'MRPerfusionNoiseLevel'
'0065' '1039' 'SH' 'MRGradRange'
'0065' '1050' 'DS' 'LocationsInAcquisition' % MRNumberOfSliceInVolume
'0065' '1051' 'SQ' 'MRVFrameSequence'}];
% elseif strncmpi(vendor, 'OtherVendor', n)
% C = [C; {}];
end

dict.group = uint16(hex2dec(C(:,1)));
Expand Down

0 comments on commit 47ad9e6

Please sign in to comment.