[Rtk-users] Reconstruct Nikon XTH320 data

[Marc Vila Oliva]

Hello Mr. Miller, 

I have tried to reconstruct your data-set but I ran into some problems
regarding the data size. 

When I launch the FDK reconstruction I get the following information:

rtkfdk --verbose -g geo500.xml -p . -r CT_121029a_quarter.mhd -o
test.mhd --dimension 500 --spacing 0.08 
Regular expression matches 1 file(s)...
Reading... MetaImage: M_ReadElementsData: data not read completely
   ideal = 3142000000 : actual = 67698688
It took 0.818956 s
Reading geometry information from geo500.xml...
Reconstructing and writing...

The reader is not able to read all the data. It reads 67698688 bytes out
of 3142000000 bytes. Then I checked if the raw data had 3142000000
bytes, but it is not the case. 
The size of CT_121029a_quarter.raw is 67698688 bytes but if you check
the header file CT_121029a_quarter.mhd, it says that the dimension of
your projections is 500 x 500 x 3142 (in total 3142000000 bytes). The
size information of the header file is inconsistent with the raw data. 

Do you really have 3142 projections? Have you cropped the raw data?

Good luck, 
Marc 

On Thu, 2013-09-12 at 21:06 -0700, M Miller wrote:
> I've been trying sporadically over the last year to reconstruct some CT data using RTK and have had only modest success. So, I'm making 
> available a small data set in the hopes that someone can point out what I'm doing wrong, or why RTK won't work for this problem.
> It can be found at:
> https://drive.google.com/folderview?id=0BwEyKtwqqtqhVDBqcncwQzVjRVk&usp=sharing
> 
> The data was acquired on a Nikon XTH320 system and also reconstructed using the vendor's CT-Pro software. Each of the projections was initially a 16bit tif image sized 2000x2000 pixels. These have been converted to attenuations, resized to 500x500, and stacked in a metaIO container. Along with the image data (mhd/raw) there are two text files created by the acquisition system that describe all of the geometry and imaging conditions. I've posted small renderings of one z-slice reconstructed with the vendor software ("CT_121029a_250.tif") and the best I've been able to get using RTK ("rtk_500.jpg"). I also included a batch file listing the rtk command line options I've been using.
> 
> I don't think there's anything else I could add that isn't in the posted configuration files, but I'd be happy to answer any questions that might help.
> Thanks
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