How I can create muli-frame DICOM from 3-D matrix

Hello everybody ! :) I'm trying to combine a sequence of 2-D images in the form 3-D matrix to a DICOM , I don't care about the metadata , I just want one big file of .dcm I tried the following:

dicomwrite(Matrix,'checkMatrix.dcm','MultiframeSingleFile','true')

and I tried the file from:

https://www.mathworks.com/matlabcentral/fileexchange/23237-read-and-write-single-file-dicom-volumes

Can You Please Help me? I feel like I missing something vital from DICOM

[Rik]

What errors are you getting? You should also be aware that many readers can't read 3D dicoms.

[alon begin]

Hello :-) when I'm running

dicomwrite(Matrix,'checkMatrix.dcm','MultiframeSingleFile','true')

I'm getting the error:

" Operands to the and && operators must be convertible to logical scalar values.

Error in dicomwrite>checkArgConsistency (line 854) options.multiframesinglefile && ...

Error in dicomwrite>write_message (line 252) checkArgConsistency(options, SOP_UID, X);

Error in dicomwrite (line 208) [status, options] = write_message(X, filename, map, metadata, options); "

It's trying to check the if operation

if (isequal(options.createmode, 'create') && ... options.multiframesinglefile && ... (size(X,4) > 1) && ... ~isSC(SOPClassUID))

    error(message('images:dicomwrite:multiFrameCreateMode'))
 line 352 in dicomwrite.m

Answer 1

[Rik]

I didn't notice at first, but you supplied true as a string, so the syntax below should at least run without errors.

dicomwrite(Matrix,'checkMatrix.dcm','MultiframeSingleFile',true)

[alon begin]

hello

you right :) but the problem on my title 'How I can create muli-frame DICOM from 3-D matrix' is still on

the next error was :

" Error using dicom_prep_ImagePixel>getPhotometricInterp (line 134) Cannot determine photometric interpretation.

Error in dicom_prep_ImagePixel (line 9) metadata.(dicom_name_lookup('0028', '0004', dictionary)) = getPhotometricInterp(metadata, X, map, txfr, dictionary);

Error in dicom_prep_metadata (line 69) metadata = dicom_prep_ImagePixel(metadata, X, map, txfr, useMetadataBitDepths, dictionary); "

The error occur on an if compression:

 if (size(X, 3) == 1)

line 70 in dicom_prep_ImagePixel.m

The value of X that is a 4-D, on size(X,3) is 54 ,the number of the frames in the sequence, I put in Matrix of : 476x616x 54 uint8

[Rik]

Some functions (like montage) want a (x,y,color,z) setup, so maybe this is such a function. I can't find something that indicates that in the doc, but it gives less information than most functions. Probably worth the try. You can use permute to change this:

IM4D=permute(IM3D,[1 2 4 3]);

[Walter Roberson]

When you dicomwrite() it is effectively mandatory to include the meta_struct or info arguments. The easiest way to create those is to use dicominfo() on a file that has the same attributes as you want for your completed file.

I say effectively mandatory because if you study enough manuals and experiment enough, it is possible to specify all the properties you need on the command line.

[alon begin]

well ..

I tried to put my effective on certain meta_struct but it still has the same mistakes but now after changed the matrix to a 4-d according to Rik Wisselink: IM4D=permute(IM3D,[1 2 4 3]);

But now in the if operation:

 if (size(X, 3) == 1)
line 70 in dicom_prep_ImagePixel.m

The X in dim 3 has the size of 2 , which also produce an error.. I tried on debug to change it to 1 and it prodouce a dicom that all it's frames are at values of 54 , (the number of frames)... :-\

[Walter Roberson]

The permute Rik showed should transform the 476 x 616 x 54 into 476 x 616 x 1 x 54 which should be acceptable. It should not somehow be making the third dimension into length 2.

Related: https://www.mathworks.com/matlabcentral/answers/44603-getphotometricinterpretation-error-when-using-multiframesinglefile-option-in-dicomwrite#answer_54909