[ITK-users] question about wiki example ResampleDICOM

Thu Sep 18 02:36:05 EDT 2014

Hi Matt,

This is indeed the observed and, based on your answer, expected behaviour.
Thank you very much for the confirmation (that's exactly what I needed!).

To avoid confusion in future, I am going to modify the corresponding
example on github and on the wiki!

Best,
Arnaud

On Wed, Sep 17, 2014 at 5:42 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi,
>
> Do to this fix [1], if the writer is re-using the GDCMImageIO, the
> writer should apply the inverse rescale / slope intercept like the
> reader applied the rescale / slope intercept when reading.  This was a
> long-standing bug that I fixed in 4.6.0.  Arnaud, if the manual
> inverse rescale / slope operation is removed, does the correct output
> result?
>
> Thanks,
> Matt
>
> [1]
> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>
> On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
> > I wrote this example many years ago…
> > 1) If the input has a non-trivial slope/intercept, the reader applies
> > the slope/intercept to the raw data.
> > 2) Rather than setting the slope/intercept in the output dicom, I
> > apply the inverse of of the slope intercept to the resampled data
> > before writing. The output dicom should not have the origin
> > slope/intercept tags.
> >
> > I'll try to verify this with Slicer, but I may be out of touch for 2
> weeks…
> >
> > Bill
> >
> >
> > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas <arnaudgelas at gmail.com>
> wrote:
> >> Hi Nick,
> >>
> >> I can confirm that with the example I get a difference of -1024 (+/- 1)
> in
> >> between the input and the output, using the ShiftScaleImage part...
> >> While without this part of code the difference is (+/-1)
> >>
> >> I would like to make sure this is the expected behaviour!?
> >>
> >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson <
> pattersonnp.work at gmail.com>
> >> wrote:
> >>>
> >>> OK, I will wait to hear the outcome of your run with the original
> example
> >>> then.
> >>>
> >>> Cheers, Nick.
> >>>
> >>>
> >>>
> >>>
> >>> On 17 Sep 2014, at 14:34, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> >>>
> >>> Nick,
> >>>
> >>> I can't roll back to previous ITK version, important patches on
> >>> itkGDCMImageIO were very recently merged...
> >>>
> >>>
> >>>
> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx
> >>>
> >>> e.g.
> >>>
> >>>
> >>>
> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273
> >>>
> >>>
> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c
> >>>
> >>>
> >>> Arnaud
> >>>
> >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson
> >>> <pattersonnp.work at gmail.com> wrote:
> >>>>
> >>>> I should also mention Arnauld that I use ITK4.5.2.  I have had many
> >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled
> back to
> >>>> ITK4.5.2.
> >>>> Nick.
> >>>>
> >>>>
> >>>>
> >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> >>>>
> >>>> Hi Matias,
> >>>>
> >>>> I guess you are referring to
> >>>>
> >>>>
> >>>>
> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
> >>>>
> >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
> >>>> v4.6.0
> >>>>
> >>>> I use the release branch of ITK
> >>>>
> >>>> ---
> >>>>
> >>>> Matt,
> >>>>
> >>>> Can you comment on this, please?
> >>>>
> >>>> Thanks
> >>>> Arnaud
> >>>>
> >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com>
> >>>> wrote:
> >>>>
> >>>> I had an issue with the resampledicom example once (all my pixel
> values
> >>>> were recalculated by adding rescaleintercept) and then downloaded the
> latest
> >>>> ITK release (4.6) and worked fine.
> >>>>
> >>>> The issue was with the GDCMIO class I beleive but was fixed somehow in
> >>>> the 4.6 version.
> >>>>
> >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <arnaudgelas at gmail.com
> >
> >>>> wrote:
> >>>>>
> >>>>> Hi all,
> >>>>>
> >>>>> I have been looking at the following wiki example:
> >>>>>
> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
> >>>>>
> >>>>> It seems to me that the section to rescale the image is not valid
> >>>>> anymore with latest ITK version (?)
> >>>>>
> >>>>>
> >>>>>
> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
> >>>>>
> >>>>> Can anyone confirm?
> >>>>>
> >>>>> Is this code validated? are output images compared to input ones in
> the
> >>>>> corresponding test?
> >>>>>
> >>>>> Thanks
> >>>>> Arnaud
> >>>>>
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> >>>
> >>
> >>
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