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

Fri Dec 6 13:13:26 EST 2013

Well, it would be nice to preserve the ability for a user to explicitly set
the slope-intercept tags for output images (not that I can think of a
particularly compelling use case of why they'd want to do so).
On Dec 6, 2013 1:10 PM, "Bill Lorensen" <bill.lorensen at gmail.com> wrote:

> 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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> >> >>
> >> >>
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> >> >>
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> >> >
> >>
> >>
> >>
> >> --
> >> Unpaid intern in BillsBasement at noware dot com
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
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> >
> >
> >
> > --
> > Brian Helba
> > Medical Imaging
> > Kitware, Inc.
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
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