[ITK-users] question about wiki example ResampleDICOM

Thu Sep 18 02:43:36 EDT 2014

Matt,

I guess there should be migration report for this fix?

Arnaud

On Thu, Sep 18, 2014 at 8:36 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> 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
>> >>>>>
>> >>>>> _____________________________________
>> >>>>> 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://public.kitware.com/mailman/listinfo/insight-users
>> >>>>>
>> >>>>
>> >>>>
>> >>>> _____________________________________
>> >>>> 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://public.kitware.com/mailman/listinfo/insight-users
>> >>>>
>> >>>>
>> >>>
>> >>>
>> >>
>> >>
>> >> _____________________________________
>> >> 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://public.kitware.com/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://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20140918/8413f6a7/attachment.html>