[Insight-users] [ITK Community] Image Intensities Changed During DICOM Read-Write-Read in ITK 3.20 vs. ITK 4.4.1

[Bill Lorensen]

Or we could just set the slope intersect to identity in the tags in
the GDCMImageIO.


On Fri, Dec 6, 2013 at 12:41 PM, Brian Helba <brian.helba at kitware.com> wrote:
> I've been looking into this whole category of GDCM issues. I'm preparing
> some more thorough bug reports for Jira, mostly related to the physical
> coordinate properties.
>
> I've also looked at the rescale issue, and it seems like the simple hack may
> actually be the best solution without some complicated new functionality in
> GDCM: if the slope-intercept tags are set for an image, just apply the
> inverse of the rescaling function to the image values right before sending
> them to GDCM. I'll try to get a patch with a good test together in the next
> few days, before the next RC.
>
>
> On Wed, Dec 4, 2013 at 1:52 PM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>>
>> I probably will not get to this before the release.
>>
>>
>> On Wed, Dec 4, 2013 at 12:12 PM, Yi-Yu Chou <yiyu.chou at gmail.com> wrote:
>> > Hi Bill,
>> >
>> > It appears the bug "Acquisition Matrix" is still not corrected when
>> > running
>> > with itk4.5_rc02.
>> > Are you going to fix it in the new released itk ?
>> >
>> > Many thanks !!
>> >
>> > Yi-Yu
>> >
>> >
>> > On Fri, Oct 18, 2013 at 8:24 PM, Constantine Zakkaroff
>> > <mnkz at leeds.ac.uk>
>> > wrote:
>> >>
>> >> Hi Bill,
>> >>
>> >> It appears the bug with slope and intercept being processed incorrectly
>> >> still shows up in ITK 4.4.2.
>> >>
>> >> Is there an explanation why in the original DICOM file rescale slope is
>> >> 7.1, but in order to see the same image stats (min, max, etc.) it needs
>> >> to
>> >> be saved with the rescale slope value of 1.0?
>> >>
>> >> Also, I believe I mentioned it a while ago, but there wasn't much
>> >> feedback
>> >> on this: some tag values get unexpected values. For example, compare
>> >> the
>> >> following tag values in the original DICOM file:
>> >>
>> >> (0010,21C0) Pregnancy Status VR: US Length: 2 Value: 4
>> >> (0018,0088) Spacing Between Slices VR: DS Length: 4 Value: 17.0
>> >> (0018,1310) Acquisition Matrix VR: US Length: 8 Value: 0 144 144 0
>> >>
>> >> and saved file:
>> >>
>> >> (0010,21C0) Pregnancy Status VR: US Length: 2 Value: 52
>> >> (0018,0088) Spacing Between Slices VR: DS Length: 2 Value: 1
>> >> (0018,1310) Acquisition Matrix VR: US Length: 12 Value: 23600 13361
>> >> 23604
>> >> 13361 23604 48
>> >>
>> >> As suggested earlier, I use the same GDCMImageIO object for reading and
>> >> writing.
>> >>
>> >> Many thanks,
>> >> Constantine
>> >>
>> >>
>> >> On 16/08/2013 19:13, Bill Lorensen wrote:
>> >>>
>> >>> Constantine,
>> >>>
>> >>> You found a bug in itk's dicom IO. I'll report it and prepare a patch
>> >>> to
>> >>> fix it for future users.
>> >>>
>> >>> As a workaround, which should work for ITK 3 and ITK4 and hopefully
>> >>> after I fix the bug:
>> >>>
>> >>> 1) If you want to retain the input dicom entries, you should create a
>> >>> GDCMImageIO and use it for both the input and output.
>> >>> 2) To work around the itk dicom bug, add these lines AFTER the stats
>> >>> filter:
>> >>>    // Set rescale slope and intercept to 1 and 0
>> >>>    imageReader0->Update();
>> >>>    typedef itk::MetaDataDictionary   DictionaryType;
>> >>>    DictionaryType & dict =
>> >>> imageReader0->GetOutput()->GetMetaDataDictionary();
>> >>>    itk::EncapsulateMetaData<std::string>( dict, "0028|1052", "0.0");
>> >>>    itk::EncapsulateMetaData<std::string>( dict, "0028|1053", "1.0");
>> >>>
>> >>> NOTE: You need to #include "itkMetaDataObject.h"
>> >>>
>> >>> I've attached the your program with all of these changes. Thanks for
>> >>> your patience,
>> >>>
>> >>> Bill
>> >>>
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>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
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>
>
>
>
> --
> Brian Helba
> Medical Imaging
> Kitware, Inc.



-- 
Unpaid intern in BillsBasement at noware dot com