iconebeam

Tomographic backprojection for cone beam geometry.

Description

This is a simple implementation of the Feldkamp-Kress-Davis (also referred to as FDK) algorithm for the reconstruction (i.e. filtered back projection) of slices from projections taken with cone beam geometry (i.e. micro-focus X ray sources).

For this demonstration we reconstruct only the central slice (z=0) of the projection that is we use the FDK as a code for the back projection of acquisitions with fan beam geometry. This allows us to exploit the matlab phantom routine to produce a synthetic projection.

For practical applications on has to write is own routine for reading the planar radiograph according to the suitable files format and correct these radiograph for the dark filed images (image registered by the detector with x ray off) and the flat filed image (x ray on and no object). Also the normalized radiograph has to the log processed and transformed into projection.

Our submission is meant to be a helpful outline for the development of a more optimized code given that Matlab offers only iradon (for parallel beams as one produced at the synchrotron beam lines) and ifanbeam routines.

The code reconstructs a volume (rather than single slices as iradon) thus an accurate evaluation of the memory necessary based on size of the planar projections is desirable.

Acknowledgement :
http://www.msri.org/publications/books/Book47/faridani/
basic FDK code
author: Faridani

• MATLAB release: MATLAB 6.5 (R13)
• Other requirements: none

[gianni schena]

Found out that one Mtlb code implementing the FDK algorithm (feldkamp.m) is available from Dr. Jeff Fessler ftp page (ftp://www.eecs.umich.edu/people/fessler/code/fbp/feldkamp.m ) and was written during August 2004.

In contrast to the our FDK that has the one outer loops over the projection and the inner loop over the slices z, the Fessler code loops over z (outer loop) and over the projections (inner loop).

[Meenal Bagla]

Hello,

I was taking a look at the filtered back projection (cone beam) algorithm you have posted on the Matlab File Exchange website. I downloaded it, in order to run it. However, it doesn't run. My version of Matlab does not recoginse the function "ifanbeam." What version of Matlab contains that function?

Is there a way I can run a demo of you code on my computer to see what it does?

I have to write a similar code that must take about 4-5 2D images of a particular 3D object from different angles and reconstruct the 3D object from those 4-5 2D images. Any ideas?

Thanks,
Meenal Bagla

[gianni schena]

One recent version of the Image Processing Toolobox (IPT) is needed in order to run the file. Indeed, the fanbean functions is used to create the sinthetic synogram and ifanbean is used to compare the central slice reconstruction

[Gianni Schena]

%%%%%
%if you do not have the statistical toolobox
% this is work-around
% old
lv=length(vct);
%b=max(vct); a=min(vct);
% percent of tail cut
ptc_L=5; ptc_H=2;% values 0 - 100
a=prctile(vct,ptc_L), b=prctile(vct,100-ptc_H),
% new ... avoids need of prctile
vct1=sort(vct,'ascend');
a=( vct1( round(ptc_L/100*lv)) ),
b=(vct1( round ((100-ptc_H)/100*lv)) ),
%%%%%

[Matt Moore]

I have a strange problem: when I run the demo, the resulting reconstruction of the central slice has what appears to two "echos" of the Shepp-Logan phantom, offset almost 90 degrees from each other. As I increase the distance (variable Radius in the demo) from the source to the center of rotation, the two echos converge to the single head phantom image that one expects. Any ideas what I am doing wrong?

[Eleonora Vidolova]

 

[hui miao]

Hello, I downloaded iconebeam, in order to run it. However, it doesn't run.
??? Undefined function or variable 'fanbeam'.

Error in ==> D:\matlab6.5\work\fdk\fdkzip\run_FDK_demo.m
On line 16 ==> [F,Floc,Fangles] = fanbeam(phant,150,'FanRotationIncrement',1, 'FanSensorGeometry' ,'line');
Any ideas? Thanks, Meenal Bagla

[gianni schena]

answer to hui miao([e-mail]) 2006-04-18
... if I have any idea ?
yes, I have a general suggestion : read the comments/instructions/suggstions enclosed with codes.

[gianni schena]

this is a good reference book on the matter,
it can be downloaded free of charge !

http://www.slaney.org/pct/pct-toc.html

Principles of Computerized Tomographic Imaging
Avinash C. Kak
School of Electrical Engineering
Purdue University
Malcolm Slaney
Originally: Schlumberger Palo Alto Research
Currently: IBM Almaden Research Center

[gianni schena]

warning:
users of iconebean code have shown that it works fine under matlab 6.5.1 (2003) but it does not work properly with later matlab versions

[gianni schena]

For Matlab ver 7 & 2006a & higher users !!!

A) in run_fdk_demo; call routine with ? (minus) sign on angles

.... iconebeamdemo(dir,fl_prefix,-Fangles,interp,filter,df,NI,step,Radius,........

B) in the function iconebeam change imshow as follows
 % shows central slice only , in figure 10
    figure(10), imshow(fliplr(vol_tmp(:,:,cnt_slc)'),[]);
 
C) in run fdk demo ; change as follows
%%%%%%
%draws slices along the x,y,z directions at the points in the vectors Sx,Sy,Sz.
else
   Img=Vol(:,:,1)'; Img=fliplr(Img);
   figure, imshow(Img,[a b]) ; title(' iconebeam');
end
%%%%