[ITK-users] question about wiki example ResampleDICOM

Thu Sep 18 13:02:55 EDT 2014

Hi Arnaud,

Great to hear it is working!

Yes, good idea on the migration guide to better communicate and
explain the development.  Here is a patch to review.

  http://review.source.kitware.com/#/c/17098/

Thanks,
Matt

On Thu, Sep 18, 2014 at 2:43 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> 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
>>
>>
>