[Insight-users] Creating a 3D image with 2D images that exhib it variable image sp acing

[Sims Richard (RKB) Clinical Scientist]

Hi Bill

 

Thanks for the info and link to the resampled data.

 

I am going to write myself a little script to do option (2) from your
list... so far I have been able to run the resample example and both the
series read/write example... now I will attempt to combine all three into
one file to resample the data to 1mm/pixel.

 

Thanks again,

Richard.

 

 

 

-----Original Message-----
From: Bill Lorensen [mailto:bill.lorensen at gmail.com] 
Sent: 28 February 2007 12:31
To: Sims Richard (RKB) Clinical Scientist
Cc: insight-users at itk.org
Subject: Re: [Insight-users] Creating a 3D image with 2D images that exhibit
variable image sp acing

 

Richard,

 

ITK does not support volumes with variable spacing. I have worked with the
Visible Human data and have handled this issue two ways:

 

1) Create multiple 3D volumes each with its own spacing.

2) Resample each 3D volume to a common spacing.

 

I resampled the fresh CT Visible Human Male and Female data sets into 1mm
pixels and converted them to DICOM. The University of Iowa hosts this data
at:

http://mri.radiology.uiowa.edu/VHDicom/index.html
<http://mri.radiology.uiowa.edu/VHDicom/index.html> 

 

Bill

 

On 2/28/07, Sims Richard (RKB) Clinical Scientist <Richard.Sims at uhcw.nhs.uk
<mailto:Richard.Sims at uhcw.nhs.uk> > wrote: 

Hi

 

I'm wondering whether anyone can help me...

 

...I have some visible human data of the head and would like to create 3D
volumes prior to performing a registration. The details of the registration
are not important at this stage, what I am more concerned with is the finer
details behind the 2D slices that create the volume. 

 

One of the datasets (frozen CT) has a constant image spacing for the 100 or
so slices I am interested in (e.g. 0.55mm/pixel), whereas the other dataset
(normal, fresh CT) has variable image spacing ( e.g. 0.55-0.75mm/pixel). I
have written a small matlab script to read in the *.txt file that is
provided with each 2D data file to create a separate *.mha file that is then
used with a script similar to the ImageSeriesReadWrite.cxx example script to
create a 3D dicom file. 

 

When I check the header of the newly created 3D dicom file there are only
one pair of values for the image spacing, presumably of the final image
slice that was used to compile it. Does the newly created dicom file contain
the correct image spacing for all slices, or are they all stored at the
displayed value (therefore rendering the file useless)? 

 

If this is the case, is there any way around it apart from creating several
smaller 3D dicom volumes?

 

Many thanks in advance,

Richard.

 

 

 

 

 

                        

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