[Insight-users] Setting the spacing of images for rigid regis tration

[Sims Richard (RKB) Clinical Scientist]

Hi Christoph

Thanks for the reply.

I actually use dicom image formats and so, as you say, the spacing is
implicitly included in the header. In this example I was using bmp/png files
(which were sourced from dicom files) and then explicitly defining the image
spacing in the code.

I have a related question which I hope you, or somebody else on the mailing
list, maybe able to help with... 

I have access to the Visible Human Project data and would like to read this
into ITK. The files have an extension according to the type of data they
contain (e.g. frozen CT data has the extension *.fro whereas proton density
data has the extension *.pd) and they also include a *.txt file that
provides all kinds of information about the data. I have attempted to read
these data files into ITK by using a metaimage header of the following type:

NDims = 2
DimSize = 512 512
ElementType = MET_USHORT
ElementSpacing = 0.898438 0.898438
ElementByteOrderMSB = False
ElementDataFile = 1055fre.raw

Where the element spacing was found in the *.txt file. Using this *.mha file
doesn't work, presumably because there is no information available regarding
the size of the header of the raw data file. As a temporary work-around I
imported the raw data file into ImageJ and specified the header size - the
data is then displayed correctly. I saved this file as a new raw data file
(in this case 1055fre.raw) and then use the above *.mha file to load it into
ITK. I then visualise the image by creating a PNG file of the data. The data
loads and appears pretty much ok, although I think I'll need to use a
rescale intensity filter. 

Is there any way the header size of the raw data file can be included in a
metaimage header file? 

Thanks in advance,
Richard.


-----Original Message-----
From: Christoph Palm [mailto:christoph.palm at web.de] 
Sent: 16 February 2007 18:34
To: Sims Richard (RKB) Clinical Scientist
Cc: 'insight-users at itk.org'
Subject: Re: [Insight-users] Setting the spacing of images for rigid
registration

Hi Richard,

it would be easiest and most correct to use an image format, that stores
your spacing implicitely, e.g. the meta image format of ITK. Reading
such images, your spacing is correctly set from the beginning.
And note, the registration is computed in real world coordinates and
is always dependend on the spacing. What image format do you use?
Otherwise use the ChangeImageInformationFilter to change the spacing
of your images.

Regards

Christoph

On Fri, 2007-02-16 at 17:13 +0000, Sims Richard (RKB) Clinical Scientist
wrote:
> Hi all
> 
>  
> 
> I have ammended one of the example codes provided with ITK to perform
> rigid registration using a Centered Rigid 2D Transform with a Mattes
> Mutual Information Metric. My fixed and moving images are both bitmaps
> which of 512x512 size but have different pixel spacing, 0.898mm/pixel
> for the fixed image and 0.527mm/pixel for the moving image. I have
> successfully registered these images using a Similarity 2D Rigid
> Transform (the moving image being re-scaled to the fixed image), but
> would like to rigidly register them without scaling by accouting for
> their different pixel spacing. I've tried to explicitly define the
> spacing of the pixels using the following code:
> 
>  
> 
> FixedImageType::SpacingType spf;
> 
> MovingImageType::SpacingType spm;
> 
> FixedImageType::PointType orf;
> 
> MovingImageType::PointType orm;
> 
>  
> 
> spm[0]=0.527344;
> 
> spm[1]=0.527344;
> 
> //spf[2]=1.000000;
> 
>  
> 
> orf[0]=0.0;
> 
> orf[1]=0.0;
> 
> //orf[2]=0.0;
> 
>  
> 
> spf[0]=0.898438;
> 
> spf[1]=0.898438;
> 
> //spm[2]=1.000000;
> 
>  
> 
> orm[0]=0.0;
> 
> orm[1]=0.0;
> 
> //orm[2]=0.0;
> 
>  
> 
> fixedImage->SetSpacing(spf);
> 
> fixedImage->SetOrigin(orf);
> 
> movingImage->SetSpacing(spm);
> 
> movingImage->SetOrigin(orm);
> 
>  
> 
> But it doesn't seem to have an effect... I'm guessing it has something
> to do with the resample image filter, but have reached a stumbling
> block... could anyone give me a pointer in the right direction?
> 
>  
> 
> Many thanks,
> 
> Richard.
> 
>  
> 
>  
> 
> 
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