How to convert tif stack to dcm series?

I have a tif file that contains 1813 pages (images). I want to convert these to DICOM files within a single series. Currently, the code I am using writes over the .dcm file during each loop. How can I fix this?

fname = 'Sample19.tif';
info = imfinfo(fname);
imageStack = [];
numberOfImages = length(info);
for k = 1:numberOfImages
    currentImage = imread(fname, k, 'Info', info);
    dicomwrite(currentImage,'gear.dcm')
    imageStack(:,:,k) = currentImage;
end 

[Amine Adjoud]

I encouter the same problem. Did you find a solution?

Answer 1

[Walter Roberson]

fname = 'Sample19.tif';
info = imfinfo(fname);
imageStack = [];
numberOfImages = length(info);
for k = 1:numberOfImages
    currentImage = imread(fname, k, 'Info', info);
    imageStack(:,:,k) = currentImage;
end 
dicomwrite(imageStack,'gear.dcm')

However, in practice you almost always need a bunch of dicom metadata. The easiest way to get that is to use dicominfo() on a dcm file that has the same kind of attributes that you are going to need, and pass the resulting metadata to dicomwrite after the file name.

[Alena Schwartz]

I updated the code so it is now:

otherinfo = dicominfo('image-000001.dcm')
fname = 'Sample19.tif';
info = imfinfo(fname);
imageStack = [];
% numberOfImages = length(info);
for k = 1:100
% for k = 1:numberOfImages
    currentImage = imread(fname, k, 'Info', info);
    imageStack(:,:,k) = currentImage;
end 

dicomwrite(imageStack,'gear.dcm',otherinfo);

I am now getting the following errors ( I am not sure how to fix this).

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 14)
    metadata = dicom_prep_ImagePixel(metadata, X, map, txfr, useMetadataBitDepths, dictionary);

Error in dicom_create_IOD (line 26)
metadata = dicom_prep_metadata(IOD_UID, metadata, X, map, options.txfr, options.usemetadatabitdepths, dictionary);

Error in dicomwrite>write_message (line 274)
        [attrs, status] = dicom_create_IOD(SOP_UID, X, map, ...

Error in dicomwrite (line 210)
    [status, options] = write_message(X, filename, map, metadata, options);

Error in convert (line 14)
dicomwrite(imageStack,'gear.dcm',otherinfo);

[Walter Roberson]

Please post the content of otherinfo

[Alena Schwartz]

otherinfo = 

  struct with fields:

                                    Filename: 'E:\Gear Model\image-000001.dcm'
                                 FileModDate: '05-Oct-2018 12:02:18'
                                    FileSize: 91494
                                      Format: 'DICOM'
                               FormatVersion: 3
                                       Width: 512
                                      Height: 512
                                    BitDepth: 12
                                   ColorType: 'grayscale'
              FileMetaInformationGroupLength: 230
                  FileMetaInformationVersion: [2×1 uint8]
                     MediaStorageSOPClassUID: '1.2.840.10008.5.1.4.1.1.2'
                  MediaStorageSOPInstanceUID: '1.2.826.0.1.3680043.8.1055.1.20111102150758825.42401392.26682309'
                           TransferSyntaxUID: '1.2.840.10008.1.2.4.91'
                      ImplementationClassUID: '1.2.826.0.1.3680043.8.1055.1'
                   ImplementationVersionName: 'dicomlibrary-100'
                SourceApplicationEntityTitle: 'DICOMLIBRARY'
                        SpecificCharacterSet: 'ISO_IR 100'
                                   ImageType: 'ORIGINAL\PRIMARY\AXIAL\HELIX'
                        InstanceCreationDate: '20061012'
                        InstanceCreationTime: '091606.000000'
                                 SOPClassUID: '1.2.840.10008.5.1.4.1.1.2'
                              SOPInstanceUID: '1.2.826.0.1.3680043.8.1055.1.20111102150758825.42401392.26682309'
                                   StudyDate: '20061012'
                             AcquisitionDate: '20061012'
                                 ContentDate: '20061012'
                                   StudyTime: '090258.000000'
                             AcquisitionTime: '085229.000000'
                                 ContentTime: '085229.750000'
                                    Modality: 'CT'
                            StudyDescription: 'CT1 abdomen'
                       ProcedureCodeSequence: [1×1 struct]
                           SeriesDescription: 'ARTERIELLE'
    ReferencedPerformedProcedureStepSequence: [1×1 struct]
                                 PatientName: [1×1 struct]
                                   PatientID: '0'
                                  PatientAge: '000Y'
                          ContrastBolusAgent: 'CONTRAST'
                                 ScanOptions: 'HELIX'
                              SliceThickness: 1
                                         KVP: 120
                        SpacingBetweenSlices: 0.5000
                      DataCollectionDiameter: 302
                                ProtocolName: 'ART.RENALES 12/Abdomen/Hx'
                      ReconstructionDiameter: 302
                          GantryDetectorTilt: 0
                                 TableHeight: 151
                           RotationDirection: 'CW'
                             XrayTubeCurrent: 400
                                    Exposure: 300
                                  FilterType: 'B'
                           ConvolutionKernel: 'B'
                             PatientPosition: 'FFS'
                            StudyInstanceUID: '1.2.826.0.1.3680043.8.1055.1.20111102150758591.92402465.76095170'
                           SeriesInstanceUID: '1.2.826.0.1.3680043.8.1055.1.20111102150758591.96842950.07877442'
                                SeriesNumber: 6168
                              InstanceNumber: 2
                        ImagePositionPatient: [3×1 double]
                     ImageOrientationPatient: [6×1 double]
                         FrameOfReferenceUID: '1.2.840.113704.1.111.3704.1160637109.3'
                               SliceLocation: -324.5000
                               ImageComments: 'JPEG 2000 lossless - Version 4.0.2 (c) Image Devices GmbH'
                             SamplesPerPixel: 1
                   PhotometricInterpretation: 'MONOCHROME2'
                                        Rows: 512
                                     Columns: 512
                                PixelSpacing: [2×1 double]
                               BitsAllocated: 16
                                  BitsStored: 12
                                     HighBit: 11
                         PixelRepresentation: 0
                                WindowCenter: [2×1 double]
                                 WindowWidth: [2×1 double]
                            RescaleIntercept: -1000
                                RescaleSlope: 1
                       LossyImageCompression: '01'
                  LossyImageCompressionRatio: 5.8667
           ScheduledProcedureStepDescription: 'CT1 abdomen'
               ScheduledProtocolCodeSequence: [1×1 struct]
                    ScheduledProcedureStepID: 'A10026177758'
           PerformedProcedureStepDescription: 'CT1 abdomen'
               PerformedProtocolCodeSequence: [1×1 struct]
                   RequestAttributesSequence: [1×1 struct]
                        RequestedProcedureID: 'A10026177757'

[Alena Schwartz]

I tried to get the dicom meta data from an DICOM image from a CT scan that I have one my computer. I am trying to convert a .tif file of a gear into .dcm files.

[Walter Roberson]

Sorry, I do not know at the moment. That is the sort of thing where I would want to use a debugger to figure out why it cannot determine the photometric interpretation.

TransferSyntaxUID: '1.2.840.10008.1.2.4.91'
ImageComments: 'JPEG 2000 lossless - Version 4.0.2 (c) Image Devices GmbH'

That is odd. Transfer Syntax 1.2.840.10008.1.2.4.91 is JPEG 2000 Image Compression, not lossless -- lossless is 1.2.840.10008.1.2.4.90, or 1.2.840.10008.1.2.4.92 (multicomponent)

[Julianna Mather]

Here are a couple of things to try/keep in mind:

• Use dicomwrite(img, filename, 'CreateMode', 'copy', info) to preserve as much metadata (in info) as possible.
• To make all of the images be part of the same series and study, use dicomuid to create a couple of UIDs and update the metadata fields info.SeriesInstanceUID and info.StudyInstanceUID.
• You'll need to update the info.ImagePositionPatient metadata value for each slice, otherwise they'll all be on top of each other. The field specifies the (x/y/z) location of the upper-left pixel in the patient coordinate system (measured in milimeters). If you know the stepping in the Z direction, this should be easy to compute and update for each loop. If not, you'll have to make something up.
• For broader compatibility, it might be a good idea to try to use a transfer syntax other than JPEG-2000. Consider setting info.TransferSyntaxUID to 1.2.840.10008.1.2.5 (for RLE lossless) or 1.2.840.10008.1.2.4.57 (for JPEG lossless).

I admit, this could be a little simpler.

[Amine Adjoud]

I encouter the same problem, did you get a solution?

[Braian Adair]

Thank you Julianna Mather you solved my four days problem!