[Insight-users] ImageWriter does not write Orientation(Direction Cosines)

[Lorensen, William E (Research)]

We should look further into this. The direction cosines should be stored as columns in the direction matrix. I thought I had verified that when I first did the implementation. Only two image io's currently support directions (nrrd and gdcmdicom). I thought I had done this correctly for dicom. The nrrd stuff is new of course. I'll look further into this.

Bill

-----Original Message-----
From: insight-users-bounces+lorensen=crd.ge.com at itk.org
[mailto:insight-users-bounces+lorensen=crd.ge.com at itk.org]On Behalf Of
Karthik Krishnan
Sent: Thursday, July 14, 2005 11:37 PM
To: Gordon Kindlmann
Cc: insight-users at itk.org; blloyd at bwh.harvard.edu
Subject: Re: [Insight-users] ImageWriter does not write
Orientation(Direction Cosines)


The MetaImage reader and writers propagate direction cosine information
now. So I think you should be able to use them fine. 

As Gordon mentioned, the transpose was happening outside Nrrd or the
particular IO mechanism in question. It was due to a bug in
itkImageFileReader.txx.

This has been fixed in CVS.

Thanks
Regards
Karthik

On Thu, 2005-07-14 at 21:19 -0400, Gordon Kindlmann wrote:
> hello,
> 
> >> Say I set the following direction cosines:
> >>
> >> 0.286406 0.118831 0.950711
> >> 0.948371 -0.176269 -0.263669
> >> 0.136249 0.977143 -0.16318
> >>
> >> then the NRRD IO writes:
> >>
> >> space directions:
> >> (0.24613,0.10212,0.817017)
> >> (0.815007,-0.151481,-0.22659)
> >> (0.681244,4.88571,-0.815902)
> >>
> >> if I read them with the NRRD IO, I read:
> >>
> >> 0.286406 0.948371 0.136249
> >> 0.118831 -0.176269 0.977143
> >> 0.950711 -0.263668 -0.163181
> >
> > Hmm.  Let me investigate this.
> 
> Okay, now I have looked into this, and I am convinced that something 
> (outside NrrdIO) is transposing the direction cosines somewhere between 
> the read and write.  I add some debugging code to the very end of 
> NrrdImageIO::Read like:
> 
>    std::vector<double> dir(3);
>    double spc;
>    for (unsigned int axi=0; axi < 3; axi++) {
>      spc = this->GetSpacing(axi);
>      dir = this->GetDirection(axi);
>      fprintf(stderr, "on read: dir[%d] = %g*(%g %g %g)\n", axi, spc,
>              dir[0], dir[1], dir[2]);
>    }
> 
> and got (via "bin/itkIOTests itkNrrdImageReadWriteTest", which as far 
> as I can tell does the simplest possible sequence of reading an image 
> and immediately writing it out, with no funny business in the middle):
> 
> on read: dir[0] = 1*(1 0 0)
> on read: dir[1] = 1*(0.707107 0.707107 0)
> on read: dir[2] = 1*(0 0 1)
> 
> which, by the way, is correct given the field in the NRRD header:
> 
>    space directions: (1,0,0) (0.707107,0.707107,0) (0,0,1)
> 
> And then, at the start of NrrdImageIO::Write, the same debugging code 
> (except for changing "read" to "write") produces:
> 
> on write: dir[0] = 1*(1 0.707107 0)
> on write: dir[1] = 1*(0 0.707107 0)
> on write: dir[2] = 1*(0 0 1)
> 
> which is wrong, and which also corresponds to the behavior Bryn 
> observed, whereby the direction cosines seem to have been transformed.
> 
> Can someone more versed than I in the details of Image IO help resolve 
> where this transposition might be happening?
> 
> Karthik, can you reproduce the same behavior in the orientation 
> handling that you just added to MetaIO?
> 
> thanks,
> Gordon
> 
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