Save binary image into .dcm

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Isabel 2014-8-19

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评论： Geoff Hayes 2014-8-26

I have segmented an organ from a CT scan (original image given in DICOM) and I would like to save the segmented image (binary one) as .dcm due to I need to use it after in other software that only read .dcm. Could someone explain me how I can do that?

Thank you in advance.

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Isabel 2014-8-22

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Hi Geoff

I used reshape because otherwise when I use dicomwrite I get the follow errors:

 % Error using dicom_prep_ImagePixel>getPhotometricInterp (line 127)
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_copy_IOD (line 31)
metadata = dicom_prep_ImagePixel(metadata, X, map, options.txfr, dictionary);
Error in dicomwrite>write_message (line 267)
        [attrs, status] = dicom_copy_IOD(X, map, ...
Error in dicomwrite (line 199)
    [status, options] = write_message(X, filename, map, metadata, options);

I was checking these errors in previous questions here, and one solution was to apply reshape.

With flipped I mean that the segmentation after convert it to .dcm is upside down with respect to the original image. And yes the origin is different; in the original image the origin is -141.715x308.715x1675.4 and voxel spacing 0.570313x0.570313x0.799927 and in the segmented image is origin -141.715x-308.715x1889 and voxel spacing 0.570313x0.570313x1

I don't know why it is happening because I'm copy the same metadata from the original image to the segmented one. Any ideas?

Thanks for your comments and help

Isabel 2014-8-26

Hi Geoff!

To flip the image I used flipdim(seg17,3) due to my image is a volume and flipud only allow 2D, but thanks for the suggestion anyway.

About my problem I finally manage to fix it. The problem was not in the way to create the DICOM file with dicomwrite, the problem was in the way that ITK-Snap read the headers when you load a CT scan. So, now everything is working fine.

Thank you for your help!