[Insight-developers] MGHImageIO bug fix, need to get the fist propagated to both ITK and Slicer

Tue Sep 24 10:41:01 EDT 2013

Hi Kent,

Thanks for the follow up.

For now let's just do the original patch. As soon as we are done releasing
Slicer 4.3.1 (happening later today), we will sync Slicer to use the same
code as ITK for MGH reading/writing.

Jc

On Tue, Sep 24, 2013 at 9:44 AM, Williams, Norman K <
norman-k-williams at uiowa.edu> wrote:

> I'll submit a pull request on Slicer.  The MGHImageIO class has gone
> through other changes in ITK; I unified the compressed/uncompressed writer
> code in single functions for readability and consistency's sake. Do you
> want me to bring Slicer into sync with ITK, or should I just submit the
> origin-writing patch?
> --
> Kent Williams norman-k-williams at uiowa.edu
>
>
>
>
>
>
> On 9/20/13 6:04 PM, "Jean-Christophe Fillion-Robin"
> <jchris.fillionr at kitware.com> wrote:
>
> >Hi Matt, Kent,
> >
> >Thanks for letting the Slicer community know about the fix.
> >
> >For the coming Slicer release, I will just cherry pick that specific
> >change. Then, we could think about using the ITK remove modules. I just
> >created an issue to keep track of it. See [1]  Could you, Hans or Matt
> >take care of submitting a pull request on Slicer
> > ?
> >
> >
> >Thanks
> >
> >Jc
> >
> >[1] http://na-mic.org/Mantis/view.php?id=3410
> >
> >
> >On Fri, Sep 20, 2013 at 6:25 PM, Matt McCormick
> ><matt.mccormick at kitware.com> wrote:
> >
> >Hi Kent,
> >
> >My vote is of course for B) -- we can add it to ITK's release branch
> >soon after, and Slicer can use the updated release branch SHA.
> >
> >Thanks,
> >Matt
> >
> >On Fri, Sep 20, 2013 at 9:25 PM, Williams, Norman K
> ><norman-k-williams at uiowa.edu> wrote:
> >> If I was just proposing a change to ITK this would be a bit easier --
> >>I'd
> >> just go through ITK's gerrit review system.
> >>
> >> As it is this has a few more moving parts.
> >>
> >> The problem was that MGHImageIO was writing out Image origins
> >>incorrectly.
> >> Eun Young Kim discovered this while using SimpleITK within Slicer to
> >>read
> >> and write MGZ files.
> >>
> >> I re-wrote the 'WriteHeader' code where it converts the origin from ITK
> >> conventions to FreeSurfer conventions, so the conversion code on the
> >>Write
> >> side matches that on the Read side.
> >>
> >> But getting this incorporated back into Slicer and ITK has more than one
> >> step.
> >>
> >> ITK:
> >> 1. Merge the pull request into the Slicer/itkMGHImageIO repository on
> >> github. The pull request is here:
> >> https://github.com/Slicer/itkMGHImageIO/pull/3
> >> 2. Get a topic through ITK Gerrit to update the SHA to match the
> >>revision
> >> of my change.
> >>
> >> SLICER:
> >>
> >> Slicer has an older version of MGHImageIO than the one used by ITK; I
> >> don't know if Slicer uses this and turns on the MGHImageIO remote module
> >> when it builds ITK.
> >> A) If Slicer uses the old code in Slicer/Libs/MGHImageIO, then this
> >>should
> >> be replaced by the code in the Github repository above.
> >> B) If Slicer uses the ITK version via the ITK remote module for
> >> itkMGHImageIO, then Š well there's a bit of a problem, as when the fix
> >> gets propogated through into ITK, it will be at the Development head for
> >> ITK, and be some time before it's part of a ITK Minor version release.
> >> Slicer no doubt picks a particular ITK version and sticks with it until
> >>a
> >> newer version comes along with sufficient new functionality and bug
> >>fixes
> >> to justify re-validating ITK all over again with Slicer.
> >>
> >> So I have the fix, I just need to know what I need to do for it to be
> >> pushed where it needs to be.
> >>
> >>
> >> --
> >> Kent Williams norman-k-williams at uiowa.edu
> >>
> >>
> >>
> >>
> >>
> >>
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