[Rtk-users] reconstruct a volume from a series of .tifs

M Miller croow at yahoo.com
Wed Oct 8 17:28:56 EDT 2014


I'm trying to reconstruct a volume from a series of .tif projections and have a few questions.
The 360 projections are each 2048x2000 floats, with transmission intensity values. The pixel spacing on the detector is 0.048mm.
The following commands do produce a volume, but the scale is wrong. The --proj_iso_* values below are guesses.

rtksimulatedgeometry.exe --output=r:\data\geo.xml --nproj=360 --arc=360 --sdd=1860 --sid=1102 --proj_iso_x=-285.496 --proj_iso_y=-260.096
rtkbackprojections.exe --geometry=r:\data\geo.xml --path=R:\data\projections -r .tif$ --output=r:\data\fromTifs.mha --bp=CudaBackProjection --spacing=.5 --dimension=500

How does rtk know the pixel spacing of the input images?
I thought I could simplify the problem by using rtksubselect to convert the tifs into a mhd/raw set before reconstruction.

rtksubselect.exe --geometry=r:\data\geo.xml --out_geometry=r:\data\geo_sub.xml --out_proj=r:\data\proj_sub.mhd --path=R:\data\projections -r .tif$

After a surprisingly long wait an mhd/raw pair are produced. 
(Why does it use so much memory? While running rtksubselect needed about 24GB, when all the projection data is <6GB and the output file is <6GB.)
The output mhd file has the ElementSpacing = 0.254. Where did that come from?
Using this mystery 0.254, the true spacing of 0.048, and the true proj_iso_x of -4.8, I calculated the working proj_iso_x value above. There must be an easier way.

So, what is the correct way to reconstruct these projections into a volume?

Thanks



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