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

[Brian Helba]

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
> >>>
> >> _____________________________________
> >> 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
> >>
> >> Please keep messages on-topic and check the ITK FAQ at:
> >> http://www.itk.org/Wiki/ITK_FAQ
> >>
> >> Follow this link to subscribe/unsubscribe:
> >> http://www.itk.org/mailman/listinfo/insight-users
> >
> >
>
>
>
> --
> 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
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/cgi-bin/mailman/listinfo/community
>



-- 
Brian Helba
Medical Imaging
Kitware, Inc.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/community/attachments/20131206/71adc186/attachment.htm>
-------------- next part --------------
_____________________________________
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

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://www.itk.org/mailman/listinfo/insight-users