How to save in dicom format

Dear All,

I have one file as attached. Then, I open it using my script as below.

Anyone can help me how to save the dataHU (as in my script) in dicom format?

clc
clear all
close all
sz = [128 128 128];
fname = 'nemaho166ab.ict';
fid = fopen(fname);
data = fread(fid,'*float'); % assuming uint
fclose(fid);
data = reshape(data,sz);
imshow3D(data)
muwater = 0.182868;
mudata = data;
dataHU = ((mudata - muwater)./ (muwater-0))*1000;
figure, imshow3D(dataHU);

[Walter Roberson]

There is a fundamental truth to using dicomwrite(): namely, that using dicomwrite() "from scratch" is a pain in the butt, to set up all of the attributes correctly. It is much easier if you have a working dicom file of the same sort as you are trying to produce, and you use dicominfo() and using the result as the "meta_struct" parameter to dicomwrite().

[mohd akmal masud]

Dear @Walter Roberson,

Let say this is my dicom attribute that want to save in this dataHU. Then how to save in dicom format?

[0008,0005] SpecificCharacterSet ISO_IR 100 CS 10

[0008,0008] ImageType [4] ORIGINAL, PRIMARY, AXIAL, CT_SOM5 SPI CS 34

[0008,0016] SOPClassUID 1.2.840.10008.5.1.4.1.1.2 UI 26

[0008,0018] SOPInstanceUID 2.16.840.1.114362.1.11979141.22403444876.563074956.450.379 UI 58

[0008,0020] StudyDate 20181115 DA 8

[0008,0021] SeriesDate 20181115 DA 8

[0008,0022] AcquisitionDate 20181115 DA 8

[0008,0023] ContentDate 20181115 DA 8

[0008,0030] StudyTime 121151.185000 TM 14

[0008,0031] SeriesTime 133355.245000 TM 14

[0008,0032] AcquisitionTime 133348.287315 TM 14

[0008,0033] ContentTime 133348.287315 TM 14

[0008,0050] AccessionNumber SH 0

[0008,0060] Modality CT CS 2

[0008,0070] Manufacturer SIEMENS LO 8

[0008,0080] InstitutionName LO 0

[0008,0090] ReferringPhysicianName PN 0

[0008,1030] StudyDescription Tumor Imaging LO 14

[Walter Roberson]

Construct a struct with field names the same as the names you show here. The field values should be character vectors for the UIDs and Manufacturer and InstitutionName and ReferringPhysicianName and StudyDescription, and should be double precision for most of the rest.

Then pass the struct in the meta_struct parameter position.

[mohd akmal masud]

Dear @Walter Roberson,

Sorry Sir, can you please write for me the example.?

[Walter Roberson]

MetaData = struct('SpecificCharacterSet', 'ISO_IR 100', ...
              'ImageType', 4, ...
              'SOPClassUID', '1.2.840.10008.5.1.4.1.1.2', ...
              %stuff
              'SeriesTime', 133355.245000, ...
              'Manufacturer', 'SIEMENS', ...
              %stuff
              );
 dicomwrite(YourData, YourFileName, MetaData)

Answer 1

[Madheswaran]

Hello Mohd Akmal Masud,

To summarize the discussions in the comments: MATLAB requires this metadata to be in a "struct" variable to create a valid DICOM file from your "dataHU" matrix.

Here is the syntax from the documentation for your context: "dicomwrite(___,meta_struct)" specifies optional metadata or file options in the structure "meta_struct". The names of fields in "meta_struct" must be the names of DICOM file attributes or options. The value of a field is the value you want to assign to the attribute or option.

The code below shows the minimal steps to create the metadata structure and save a single slice of your data.

% your existing code
% clc
% clear all
% ... (your code goes here)
% dataHU = ...

% create the metadata structure 
% The field names (e.g., 'StudyDescription') must match DICOM attribute names.
% This example uses a few attributes from the list you provided.
meta = struct();
meta.StudyDescription = 'Tumor Imaging';
meta.Modality = 'CT';
meta.Manufacturer = 'SIEMENS';
meta.PatientID = '12345'; % A DICOM file requires some patient info

% selecting the first slice to store 
slice_data = dataHU(:, :, 1);
dicomwrite(slice_data, 'output_slice.dcm', meta);

For more information, refer to the following MathWorks documentation: https://mathworks.com/help/images/ref/dicomwrite.html

I hope this helps!