[Insight-developers] Re: Update on GE5 Image Reading (STILL NEED
SCANS!)
Bill Lorensen
bill.lorensen at gmail.com
Thu Oct 25 08:23:04 EDT 2007
Steve,
I have those files. The other ones I gathered 10 years ago I think, maybe
longer. They were off an old Signa.
Bill
On 10/25/07, Steve Pieper <pieper at bwh.harvard.edu> wrote:
>
> Bill -
>
> You gave me some phantom data a while ago that I put on the wiki - are
> these the ones you mean? They all work with the ITK readers in
> slice2.6. We didn't have GE files for these and they are all
> axis-aligned acquisitions I believe.
>
> http://www.na-mic.org/Wiki/index.php/OrientationTestData
>
> -Steve
>
> Bill Lorensen wrote:
> > Steve,
> >
> > It would be great if he could scan a phantom. There used to be a GE
> > phantom that was made of Plexiglas. I had scans of it in every
> > direction, but I have no idea where the data is.
> >
> > Bill
> >
> > On 10/24/07, *Steve Pieper* <pieper at bwh.harvard.edu
> > <mailto:pieper at bwh.harvard.edu>> wrote:
> >
> > I talked with Marek today and in a couple weeks he'll have some
> scanner
> > time and we'll try the following:
> >
> > - acquire various scan orientations (including oblique) of the same
> > subject
> > - acquire both structural and dwi
> > - save as both dicom and ge native
> >
> > This will give us a nice data set for debugging these issues and the
> > related (but even *more* complex!) issues with diffusion sequences.
> >
> > Thanks everybody for digging into this,
> > -Steve
> >
> > p.s. Go Sox!
> >
> > Bill Lorensen wrote:
> > > It was raining today and my golf buddy is in Florida for the
> > winter...
> > >
> > > Retired Bill
> > >
> > >
> > > On 10/24/07, *Hans Johnson* <hans-johnson at uiowa.edu
> > <mailto:hans-johnson at uiowa.edu>
> > > <mailto:hans-johnson at uiowa.edu <mailto:hans-johnson at uiowa.edu>>>
> > wrote:
> > >
> > > Bill,
> > >
> > > THANKS. Your efforts on this are greatly appreciated. I'll
> > try to
> > > test it out later this week.
> > >
> > > Hans
> > > --
> > > Hans J. Johnson, Ph.D.
> > > Hans-johnson at uiowa.edu <mailto:Hans-johnson at uiowa.edu>
> > <mailto:Hans-johnson at uiowa.edu <mailto:Hans-johnson at uiowa.edu>>
> > >
> > > 278 GH
> > > The University of Iowa
> > > Iowa City, IA 52241
> > > (319) 353 8587
> > >
> > >
> > >
> >
> ------------------------------------------------------------------------
> > > *From: *Bill Lorensen < bill.lorensen at gmail.com
> > <mailto:bill.lorensen at gmail.com>
> > > <mailto:bill.lorensen at gmail.com
> > <mailto:bill.lorensen at gmail.com>>>
> > > *Date: *Wed, 24 Oct 2007 17:38:29 -0400
> > > *To: *kent williams <norman-k-williams at uiowa.edu
> > <mailto:norman-k-williams at uiowa.edu>
> > > <mailto:norman-k-williams at uiowa.edu
> > <mailto:norman-k-williams at uiowa.edu>>>
> > > *Cc: *ITK < insight-developers at itk.org
> > <mailto:insight-developers at itk.org>
> > > <mailto:insight-developers at itk.org
> > <mailto:insight-developers at itk.org>>>, Hans Johnson
> > > <hans-johnson at uiowa.edu <mailto:hans-johnson at uiowa.edu>
> > <mailto:hans-johnson at uiowa.edu <mailto:hans-johnson at uiowa.edu>>>,
> Steve
> > > Pieper < pieper at bwh.harvard.edu
> > <mailto:pieper at bwh.harvard.edu> <mailto:pieper at bwh.harvard.edu
> > <mailto:pieper at bwh.harvard.edu>>>
> > > *Subject: *Re: Update on GE5 Image Reading (STILL NEED
> SCANS!)
> > >
> > >
> > > Kent,
> > >
> > > My changes sort the files also, if necessary. Also, the
> origin
> > > computation was wrong.
> > >
> > >
> > > Bill
> > >
> > > On 10/24/07, *kent williams* < norman-k-williams at uiowa.edu
> > <mailto:norman-k-williams at uiowa.edu>
> > > <mailto:norman-k-williams at uiowa.edu
> > <mailto:norman-k-williams at uiowa.edu>>> wrote:
> > >
> > > Mea Maxima Culpa -- the GE file formats Image I/O stuff
> > is the
> > > very first
> > > ITK code I wrote, and there is more than a little
> ugliness
> > > involved there
> > > unfortunately. I was converting code from BRAINS2 to the
> > ITK way.
> > >
> > > Anyway, I have a fix that I can check in that makes
> > images look
> > > much better.
> > > As near as I can figure, the sorting of slice files was
> > > backwards in some
> > > cases. It was even worse than that really --
> > itk::GE5ImageIO
> > > was looking at
> > > fields in the GE5/Signa/Genesis file header that don't
> really
> > > mean what the
> > > code thought it meant.
> > >
> > > Someone (Bill Lorensen is one suspect) added the code to
> > > generate direction
> > > cosines directly from the GE5 file header, so I started
> using
> > > that instead
> > > of undocumented fields in the header to recover the
> > orientation.
> > > That
> > > DirCosine code is as far as I know correct.
> > >
> > > But, the test images were coming in swapped in one
> > dimension or
> > > another.
> > > What I finally figured out is that the code that sorted
> > the 2D
> > > files before
> > > moving data into a 3D buffer wasn't using the right sort
> > order,
> > > at all. So I
> > > added code to set the sort order right, based on the
> image
> > > orientation.
> > >
> > > I THINK I have it licked but I'm still not finding good,
> > > unambiguous test
> > > data. I can tell where the top of the skull and the nose
> > are,
> > > but bilateral
> > > symmetry means I can't tell when there's a L/R swap.
> > >
> > > Fucang was kind enough to find me a few good sample
> > files. But
> > > does anyone
> > > have any GE5 files where there's some indication of which
> is
> > > left and right?
> > > Something like the 'vitaman E cap on the left temple'
> trick
> > > would be ideal.
> > >
> > > Speaking of sample files:
> > >
> > > This directory
> > > http://128.196.98.224/Public/Imaging/Event/MGH/New/
> > > <http://128.196.98.224/Public/Imaging/Event/MGH/New/> is
> > > supposed to be an example of an axially oriented GE5
> > file. If
> > > you load it
> > > into Slicer3 (for example) it looks way way ugly. Not
> > clear to
> > > me why, but
> > > Slicer3 displays the volume as a skewed frustrum, as
> though
> > > every coronal
> > > slice is offset in the Y direction from it's neighbors.
> > >
> > >
> > >
> > >
> >
> >
>
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