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problem with DicomCleaner

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  • david.pinelle
    I am considering using DicomCleaner as part of a utility I am developing to transfer PACS images to our teaching file server. I am mainly interested in the
    Message 1 of 4 , Apr 28 11:50 AM
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      I am considering using DicomCleaner as part of a utility I am developing to transfer PACS images to our teaching file server. I am mainly interested in the Blackout tool, and I have tried it on a range of images, but I am running into some problems.

      When I save some Monochrome images, the appearance of the image changes in the blackout window at save time--the colors invert (or seem to, it might not be as simple as an inversion), and the image, which is primarily black, becomes white and the details of the image are no longer visible. This transformation is also found in the saved image.

      I have also tried several other images, from different modalities and from different sources. The strange inversion does not always occur. However, once the images have been saved, I am unable to open them with most viewers. I cannot open with the Sante free viewer or with EZDicom (which throws and error when I try to open them).

      When I upload the images to RSNA's MIRC teaching file server, some are ignored, and the ones that are displayed are not displayed properly (JPEGS are not generated properly). MIRC is usually pretty forgiving, and can usually handle DICOM files that are not displayed properly elsewhere.

      I appreciate any help or advice that anyone can offer.

      Best regards,
      David
    • dclunie99
      Can you upload a sample that causes the problem to: http://public.me.com/dclunie and I will take a look and see if I can reproduce the problem. What build,
      Message 2 of 4 , Apr 28 2:09 PM
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        Can you upload a sample that causes the problem to:

        "http://public.me.com/dclunie"

        and I will take a look and see if I can reproduce the
        problem.

        What build, and what JRE version and what OS are you using ?

        David

        --- In pixelmed_dicom@yahoogroups.com, "david.pinelle" <david.pinelle@...> wrote:
        >
        > I am considering using DicomCleaner as part of a utility I am developing to transfer PACS images to our teaching file server. I am mainly interested in the Blackout tool, and I have tried it on a range of images, but I am running into some problems.
        >
        > When I save some Monochrome images, the appearance of the image changes in the blackout window at save time--the colors invert (or seem to, it might not be as simple as an inversion), and the image, which is primarily black, becomes white and the details of the image are no longer visible. This transformation is also found in the saved image.
        >
        > I have also tried several other images, from different modalities and from different sources. The strange inversion does not always occur. However, once the images have been saved, I am unable to open them with most viewers. I cannot open with the Sante free viewer or with EZDicom (which throws and error when I try to open them).
        >
        > When I upload the images to RSNA's MIRC teaching file server, some are ignored, and the ones that are displayed are not displayed properly (JPEGS are not generated properly). MIRC is usually pretty forgiving, and can usually handle DICOM files that are not displayed properly elsewhere.
        >
        > I appreciate any help or advice that anyone can offer.
        >
        > Best regards,
        > David
        >
      • david.pinelle
        Hi David, I am running Windows XP Pro SP3. My JRE version is 1.6 (1.6.0_16). I initially installed the 3.9MB package that requires Java 1.5 or later. Re:
        Message 3 of 4 , Apr 29 2:42 PM
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          Hi David,
          I am running Windows XP Pro SP3.

          My JRE version is 1.6 (1.6.0_16). I initially installed the 3.9MB package that requires Java 1.5 or later.

          Re: DicomCleaner build. I was not able to find version information in the application or in the ReadMe files. I downloaded the packages on Monday (April 26) from http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html

          I just downloaded and installed the 45MB package that includes everything (libraries, JRE). This seems to have fixed most of my problems.

          There is still one unresolved issue that pops up when I try to use the blackout tool on one of my testing images. I uploaded the image (brain_005.dcm) to a folder called "From DavidP". When I use the blackout tool and press the save button, the black and white distribution changes dramatically (inverts?). This is visible in the blackout editor window and in the resulting file.

          Thanks and best regards,
          David


          --- In pixelmed_dicom@yahoogroups.com, "dclunie99" <dclunie@...> wrote:
          >
          > Can you upload a sample that causes the problem to:
          >
          > "http://public.me.com/dclunie"
          >
          > and I will take a look and see if I can reproduce the
          > problem.
          >
          > What build, and what JRE version and what OS are you using ?
          >
          > David
          >
          > --- In pixelmed_dicom@yahoogroups.com, "david.pinelle" <david.pinelle@> wrote:
          > >
          > > I am considering using DicomCleaner as part of a utility I am developing to transfer PACS images to our teaching file server. I am mainly interested in the Blackout tool, and I have tried it on a range of images, but I am running into some problems.
          > >
          > > When I save some Monochrome images, the appearance of the image changes in the blackout window at save time--the colors invert (or seem to, it might not be as simple as an inversion), and the image, which is primarily black, becomes white and the details of the image are no longer visible. This transformation is also found in the saved image.
          > >
          > > I have also tried several other images, from different modalities and from different sources. The strange inversion does not always occur. However, once the images have been saved, I am unable to open them with most viewers. I cannot open with the Sante free viewer or with EZDicom (which throws and error when I try to open them).
          > >
          > > When I upload the images to RSNA's MIRC teaching file server, some are ignored, and the ones that are displayed are not displayed properly (JPEGS are not generated properly). MIRC is usually pretty forgiving, and can usually handle DICOM files that are not displayed properly elsewhere.
          > >
          > > I appreciate any help or advice that anyone can offer.
          > >
          > > Best regards,
          > > David
          > >
          >
        • David Clunie
          Interesting. The image you sent has the following characteristics: - it is signed (pixel representation == 1) - it has a bit depth of 16 - pixel values
          Message 4 of 4 , Apr 30 10:08 AM
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            Interesting.

            The image you sent has the following characteristics:

            - it is signed (pixel representation == 1)
            - it has a bit depth of 16
            - pixel values actually range from 0 to 0x03a4 (932 dec)
            - it has illegal window center and width values both 0

            DicomCleaner chooses the value to use to replace blacked
            out pixels as the lowest possible pixel value given the
            signedness and bit depth, 0x8000 (-32768 dec).

            Then given the absence of valid window information, the
            display code tries to guess a window based on the range
            of the pixel data, which is now -32768 to 932 dec, as
            opposed to 0 to 932 dec, hence it looks white (though
            the pixel data itself is actually fine).

            Other views would likely do the same if they try to guess
            a window based on range.

            Whilst it might be appropriate to actually "search" the
            pixel data (for each frame or each image or all images
            in a series) to be sure there are actually no -ve values
            even though the data claims to be signed, or one could
            add valid window values, or one could change the sign
            during blackout, though this is not always
            valid, so I think it is probably best to simply give the
            user the option to:

            - use the pixel padding value in the header, if any, or

            - force the blackout replacement value to be zero

            I have put an experimental version of pixelmed.jar at:

            "http://www.dclunie.com/pixelmed/software/20100430_experimental/"

            that does this ... copy it into place wherever you have
            installed what you are using.

            The default is to use the pixel padding value in the header,
            which happens to be zero for this image.

            Let me know if this solves your problem in the general case,
            without introducing more problems for other images.

            Turning off both options will go back to the way it always
            has been (lowest possible value).

            David

            PS. Where did you get this image or how did you create it ?

            It looks like it has been created using a version of my old
            dicom3tools convertors, but using an illegal root UID of 0.0.0.0.

            If so, I should probably check to make sure those tools are not
            inserting illegal (zero valued) window attributes.

            On 4/29/10 5:42 PM, david.pinelle wrote:
            > Hi David,
            > I am running Windows XP Pro SP3.
            >
            > My JRE version is 1.6 (1.6.0_16). I initially installed the 3.9MB package that requires Java 1.5 or later.
            >
            > Re: DicomCleaner build. I was not able to find version information in the application or in the ReadMe files. I downloaded the packages on Monday (April 26) from http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html
            >
            > I just downloaded and installed the 45MB package that includes everything (libraries, JRE). This seems to have fixed most of my problems.
            >
            > There is still one unresolved issue that pops up when I try to use the blackout tool on one of my testing images. I uploaded the image (brain_005.dcm) to a folder called "From DavidP". When I use the blackout tool and press the save button, the black and white distribution changes dramatically (inverts?). This is visible in the blackout editor window and in the resulting file.
            >
            > Thanks and best regards,
            > David
            >
            >
            > --- In pixelmed_dicom@yahoogroups.com, "dclunie99"<dclunie@...> wrote:
            >>
            >> Can you upload a sample that causes the problem to:
            >>
            >> "http://public.me.com/dclunie"
            >>
            >> and I will take a look and see if I can reproduce the
            >> problem.
            >>
            >> What build, and what JRE version and what OS are you using ?
            >>
            >> David
            >>
            >> --- In pixelmed_dicom@yahoogroups.com, "david.pinelle"<david.pinelle@> wrote:
            >>>
            >>> I am considering using DicomCleaner as part of a utility I am developing to transfer PACS images to our teaching file server. I am mainly interested in the Blackout tool, and I have tried it on a range of images, but I am running into some problems.
            >>>
            >>> When I save some Monochrome images, the appearance of the image changes in the blackout window at save time--the colors invert (or seem to, it might not be as simple as an inversion), and the image, which is primarily black, becomes white and the details of the image are no longer visible. This transformation is also found in the saved image.
            >>>
            >>> I have also tried several other images, from different modalities and from different sources. The strange inversion does not always occur. However, once the images have been saved, I am unable to open them with most viewers. I cannot open with the Sante free viewer or with EZDicom (which throws and error when I try to open them).
            >>>
            >>> When I upload the images to RSNA's MIRC teaching file server, some are ignored, and the ones that are displayed are not displayed properly (JPEGS are not generated properly). MIRC is usually pretty forgiving, and can usually handle DICOM files that are not displayed properly elsewhere.
            >>>
            >>> I appreciate any help or advice that anyone can offer.
            >>>
            >>> Best regards,
            >>> David
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