[Insight-users] Question on MHD format

[Karthik Krishnan]

No.. DimSize should refer to the size of your image. The point is that 
you are merely making sure that both volumes have the same location in 
real world (physical) coordinates.

For instance if you had Volume 1:  256 x 256 x 256 with a spacing of 1.0 
1.0 1.0

NDims = 3
DimSize = 256 256 256
ElementSpacing = 1.0 1.0 1.0
Position = 0.0 0.0 0.0
ElementByteOrderMSB = False
ElementType = MET_SHORT
ElementDataFile = Volume1.raw


Volume 2 that represented the extents of some anatomical region from 
(100, 100, 100)- (120, 120, 120)

NDims = 3
DimSize = 21 21 21
ElementSpacing = 1.0 1.0 1.0
Position = 100.0 100.0 100.0
ElementByteOrderMSB = False
ElementType = MET_SHORT
ElementDataFile = Volume2.raw

Then for any physical point p, you would get the same pixel by

volume1->TransformPhysicalPointToIndex( p, idx1 );
volume1->GetPixel(idx1);  

volume2->TransformPhysicalPointToIndex( p, idx2 );
volume2->GetPixel(idx2);  

In other words p is the same physical point, but its index in the two 
volumes, idx1 and idx2 will be different.

Does this make it clear ?

-karthik


Tim Soper wrote:

>Karthik,
>  Thanks for your reply, I'm almost there.  If I used
>the position tag, how then would I specify the size of
>the sub region? (I assume the DimSize tag still needs
>to refer to the size of the  whole image). 
>
>-Tim-
>
>--- Karthik Krishnan <Karthik.Krishnan at kitware.com>
>wrote:
>
>  
>
>>The position tag lets you represent subregions.
>>
>>Here's the header
>>...
>>...
>>Position = -10.5 -10.5 -10.5
>>...
>>
>>That means the origin of this image is at -10.5. So
>>if you had a small 
>>image that represented a subregion of a larger
>>image, you could have the 
>>subregion handled by itk::Image at the right
>>physical location in the 
>>image by specifying its origin at the appropriate
>>position. We do this 
>>often during registration where images from
>>different modalities might 
>>have different physical extents.
>>
>>HTH
>>karthik
>>
>>Luis Ibanez wrote:
>>
>>    
>>
>>>Hi Tim,
>>>
>>>An easier way of saving disk space is by
>>>      
>>>
>>compressing
>>    
>>
>>>your images.
>>>
>>>The MetaImage formal let you gzip your raw files.
>>>
>>>What you will have to do is to edit the .mhd files
>>>and update the name of the .raw file in order to
>>>include the additional extension  .raw.gz (or any
>>>other name that you decide to give to the
>>>      
>>>
>>compressed
>>    
>>
>>>file).
>>>
>>>This compression works quite well for labeled
>>>      
>>>
>>images
>>    
>>
>>>since it is based on Run Length Encoding. It
>>>      
>>>
>>doesn't
>>    
>>
>>>work quite well on noisy images though....
>>>
>>>Note that gzip compression is lossless, so you
>>>      
>>>
>>shouldn't
>>    
>>
>>>have any concerns about degradation of the image
>>>      
>>>
>>data
>>    
>>
>>>due to the compression.
>>>
>>>Please give it a try to compress the raw files
>>>      
>>>
>>(and
>>    
>>
>>>modify their name accordingly in the .mhd files)
>>>      
>>>
>>and
>>    
>>
>>>let us know if you find any problems.
>>>
>>>
>>>
>>>    Thanks
>>>
>>>
>>>
>>>       Luis
>>>
>>>
>>>
>>>
>>>=======================
>>>Tim Soper wrote:
>>>
>>>      
>>>
>>>>Hi,
>>>>   I intersted in finding a way to reduce the
>>>>        
>>>>
>>space
>>    
>>
>>>>taken up on my hard drive by a number of raw data
>>>>files roughly 512^3 in size. I find that I am
>>>>        
>>>>
>>making
>>    
>>
>>>>several images that are both clipped versions of
>>>>        
>>>>
>>the
>>    
>>
>>>>original large image as well as creating
>>>>        
>>>>
>>segmented
>>    
>>
>>>>images of these original images for different
>>>>applications.
>>>>   I would like to keep these large images, but I
>>>>        
>>>>
>>am
>>    
>>
>>>>wondering if there is a way to specify a desired
>>>>region of an image through some sort of MetaImage
>>>>header tag. For example, if I wanted just a
>>>>        
>>>>
>>clipped
>>    
>>
>>>>portion of my original image, say 256^3 in size,
>>>>        
>>>>
>>can I
>>    
>>
>>>>simply make a new header file that specifies that
>>>>sub-region of the original image, but referencing
>>>>        
>>>>
>>the
>>    
>>
>>>>same large ElementDataFile? This would preclude
>>>>creation of multiple data files with redundant
>>>>        
>>>>
>>data.
>>    
>>
>>>>   Also, It would be convenient if rather than
>>>>creating new images of segmented regions of my
>>>>original image, I could add another raw data file
>>>>reference to the header that contained an image
>>>>        
>>>>
>>mask
>>    
>>
>>>>of the segmented regions rather than rewriting
>>>>        
>>>>
>>the
>>    
>>
>>>>same image data again. I have looked through the
>>>>        
>>>>
>>MHD
>>    
>>
>>>>file formats and there doesn't appear to be any
>>>>        
>>>>
>>tags
>>    
>>
>>>>that suit this function.
>>>>Please let me know if this is possible.
>>>>
>>>>Tim
>>>>
>>>>
>>>>        
>>>>
>>__________________________________________________
>>    
>>
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>>>>
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>>
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>>>>
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>>    
>>
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>>>>
>>>>
>>>>        
>>>>
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>>>      
>>>
>
>
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