[Insight-developers] Re: Update on GE5 Image Reading (STILL NEED SCANS!)

[Bill Lorensen]

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> 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
>
> 278 GH
> The University of Iowa
> Iowa City, IA 52241
> (319) 353 8587
>
>
> ------------------------------
> *From: *Bill Lorensen <bill.lorensen at gmail.com>
> *Date: *Wed, 24 Oct 2007 17:38:29 -0400
> *To: *kent williams <norman-k-williams at uiowa.edu>
> *Cc: *ITK <insight-developers at itk.org>, Hans Johnson <
> hans-johnson at uiowa.edu>, Steve Pieper <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> 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/ 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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