[Insight-developers] Analyze IO

[Jim Miller]

Stephen,

For your particular case, can you assign an (arbitrary) orientation to your
microscopy images to satisfy the Analyze writer?  For instance, your
microscopy images could default to "axials".

I think Hans is on the right track here.  The Analyze format was meant for
medical images and Analyze the application is very careful about the
orientation of imagery.  Unfortunately, there are a lot of applications that
claim to support the Analyze file format but end up screwing up the
orientations, making the files produced "unusable" for other applications.
This in turn gives the Analyze format a bad name, one that it does not
deserve.  Where possible, we should try to do the right thing so that ITK
does not become one of the tools producing bad Analyze files.

Coincidently, we hit upon this same "bug" this week.  Recompiled some code
that was sitting on shelf for a few months and it no longer ran.  At first,
we were rather upset.  But in our case, a fix to our program's use of the
ResampleImageFilter (we were actually using it incorrectly) worked around
the change in the AnalyzeImageIO and made our code more correct.

Jim



On 2/24/07, Stephen R. Aylward <Stephen.Aylward at kitware.com> wrote:
>
> Hi Hans,
>
> According to the ITK survey, 45% of ITK users are using ITK outside of
> the medical field.
> http://www.itk.org/Wiki/2006_Survey_Summary#Areas_of_Use_of_the_Toolkit
>
> If ITK only did anatomic images, I'd probably agree that an undefined
> image orientation is not needed - but the solution to the lack of an
> orientation should probably be fixed in the readers and image sources
> and not in the writers.
>
> For me, the problem came about because of microscopy work that I began
> at UNC.  They asked for some changes, I did them, recompiled using the
> latest ITK, and now the programs no longer work for them.   They can no
> longer create analyze formatted images which are required by another
> program in their pipeline.
>
> The changes to itkAnalyze mean that we can no longer use analyze for
> microscopy images, for data from any other domain for which image
> orientation is (and should be) undefined, for images that originated as
> stacks of jpegs, etc in which orientation is undefined, for
> phantom/simulated data studies, etc.
>
> Stephen
>
> Hans J. Johnson wrote:
> > Stephan,
> >
> > The problem with this is that it introduces the very real possiblility
> of
> > getting right/left swaps in your images.  The ITK implementation was
> written
> > to meet the file format definition as specified by the original
> developers
> > (i.e. Mayo clinic as part of the Analyze program).   The bug fixes
> occurred
> > close to the time when the switch from metadata orientation to direction
> > cosines was done.  This is mostly because that is when the bug was
> > discovered, isolated, and a fix was made.  The original buggy meta-data
> code
> > was written prior to images having a well defined definition concept of
> > orientation, and during the implementation of the orientation code (via
> > direction cosines) this definition became clear and well defined across
> all
> > file format readers.
> >
> > The behavior did change, but it was a bug fix.
> >
> > I have very strong feelings on this because analyze files that are
> written
> > to disk with ambiguity have cost me weeks of time tracking down
> problems.
> > Because of this dangerous situation, I believe quite strongly that any
> file
> > format that claims to respect orientation should do so consistently
> across
> > all file formats.
> >
> > You proposal below would map the following 3 direction cosign inputs to
> the
> > analyze file filter correctly:
> >
> > itk::SpatialOrientationAdapter<3>::DirectionType SAGdir=
> >
> SpatialOrientationAdapter<3>().ToDirectionCosines(itk::SpatialOrientation::I
> > TK_COORDINATE_ORIENTATION_PIR);
> > SAGITTAL 133124
> > 0 0 1
> > -1 0 0
> > 0 1 0
> >
> > itk::SpatialOrientationAdapter<3>::DirectionType CORdir=
> >
> itk::SpatialOrientationAdapter<3>().ToDirectionCosines(itk::SpatialOrientati
> > on::ITK_COORDINATE_ORIENTATION_RIP);
> > CORONAL 264194
> > 1 0 0
> > 0 0 -1
> > 0 1 0
> >
> > itk::SpatialOrientationAdapter<3>::DirectionType AXIdir=
> >
> SpatialOrientationAdapter<3>().ToDirectionCosines(itk::SpatialOrientation::I
> > TK_COORDINATE_ORIENTATION_RPI);
> > AXIAL 525314
> > 1 0 0
> > 0 -1 0
> > 0 0 1
> >
> > ===============================
> > But the other 45 possible orientations of a 3D dataset would also map to
> the
> > RPI definition.  This means that I could only trust SAGITTAL and CORONAL
> > image definitions, and would be forced to assume all other definitions
> are
> > "best guesses"
> >
> > ###############################
> > ###############################
> > ###############################
> > Another acceptable solution would be to reorient the image data for
> those
> > other 45 possibilities to the RPI orientation prior to writing.  I
> assume
> > that the main problem is that the default direction cosign of
> > 1 0 0
> > 0 1 0
> > 0 0 1
> >
> > Is not a legal tag for analyze file formats.
> >
> > ###############################
> > ###############################
> > ###############################
> > Finally, there is a bit of a compromise.  I was originally advised not
> to
> > use analyze orient codes of "3,4,5,6" because they are so often mis-used
> by
> > improper 3rd party analyze image implementors:
> >
> > typedef enum _analyze75_orient_code
> >   {
> >     a75_transverse_unflipped = 0,
> >     a75_coronal_unflipped = 1,
> >     a75_sagittal_unflipped = 2,
> >     a75_transverse_flipped = 3,
> >     a75_coronal_flipped = 4,
> >     a75_sagittal_flipped = 5,
> >     a75_orient_unknown = 6
> >   }
> >   analyze_75_orient_code;
> >
> > Conversations with the Analyze folks indicated that to respect the
> original
> > intent of the file format, that orient codes of "3,4,5,6" were only to
> be
> > used internal to the Analyze program for display purposes, and were
> never
> > supposed to be written to disk.
> >
> > I would be quite comfortable with having this implementation put into
> place.
> > I would like to put a prohibition on reading or writing orientaiton
> codes
> > with the unknown orientation flag.  Again force re-orientation of the
> image
> > to a valid (preferably code 0,1,2) orientation before writing.
> >
> > Sorry to be so draconian about this, but I have been very embarrassed
> > because I depended on ITK getting these orientation done
> correctly.  When
> > using ITK to convert dicom images to both nifti and analyze images,
> about 5%
> > of the 500 images were right left swapped when the nifti and analyze
> images
> > were loaded with ITK tools.  I confirmed the problem by using a simple
> image
> > difference program, and the dicom-nifti always gave 0, but 5% of the
> > nifti-analyze showed the right left swap.
> >
> > I'm leaving town tomorrow, so won't be able to put this into place, but
> > perhaps I can get some help? If this is something that needs to be done
> > quickly, Kent Williams should have time during the middle to end of this
> > week to work on the changes and tests.  There should be a test to ensure
> > that only valid accepted codes can be read and written to disk.  If the
> > difference between reading and writing analyze or nifti (or any other
> > sufficiently tagged format Meta/Dicom) should be un-ambiguous.
> >
> > Ok...enough ranting ;)
> >
> > Regards,
> > Hans
> >
> >
> >
> > On 2/24/07 10:49 AM, "Stephen R. Aylward" <Stephen.Aylward at Kitware.com>
> > wrote:
> >
> >> Hi,
> >>
> >> The behavior of the Analyze writer has changed.   Now if the
> orientation
> >> of the image isn't known, an exception is thrown.
> >>
> >> The changes are related to the switch from metadata orientation usage
> to
> >> oriented image usage.
> >>
> >> I suggest that if the orientation is unknown/undefined, then we throw a
> >> warning, but continue under the assumption of RPI (the default used in
> >> other cases).   Only if the orientation is explicit and not a supported
> >> type should we throw an exception.
> >>
> >> I've make the changes in my local version and can forward them to
> anyone
> >> with cvs access.
> >>
> >> Stephen
> >
> >
>
> --
> =============================================================
> Stephen R. Aylward, Ph.D.
> Chief Medical Scientist
> Kitware, Inc. - Chapel Hill Office
> http://www.kitware.com
> Phone: (518)371-3971 x300
> _______________________________________________
> Insight-developers mailing list
> Insight-developers at itk.org
> http://www.itk.org/mailman/listinfo/insight-developers
>
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