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fdk - Online in the Cloud

Run fdk in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command fdk that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


fdk - cone-beam reconstruction from projections using the FDK algorithm

The term FDK refers to the authors Feldkamp, Davis, and Kress who wrote the seminal paper
"Practical cone-beam algorithm" in 1984. Their paper describes a filtered back-projection
reconstruction algorithm for cone-beam geometries. The fdk program in plastimatch is an
implmenetation of the FDK algorithm.

FDK USAGE


The fdk program takes a directory of 2D projection images as input, and generates a single
3D volume as output.

The command line usage is:

Usage: fdk [options]
Options:
-A hardware Either "cpu" or "cuda" (default=cpu)
-a "num ((num) num)" Use this range of images
-r "r1 r2 r3" Set output resolution (in voxels)
-f filter Either "none" or "ramp" (default=ramp)
-s scale Scale the intensity of the output file
-z "s1 s2 s3" Physical size of the reconstruction (in mm)
-I indir The input directory
-O outfile The output file

The usage of the fdk program is best understood by following along with the tutorials:
fdk_tutorial_i and fdk_tutorial_ii.

INPUT FILES


Three different formats of input files are supported. These are:

· Pfm format image files with geomtry txt files

· Raw format image files with geomtry txt files

· Varian hnd files

The pfm and raw files are similar, in that they store the image as an array of 4-byte
little-endian floats. The only difference is that the pfm file has a header which stores
the image size, and the raw file does not.

Each pfm or raw image file must have a geometry file in the same directory with the .txt
extension. For example, if you want to use image_0000.pfm in a reconstruction, you should
supply another file image_0000.txt which contains the geometry. A brief description of
the geometry file format is given in proj_mat_file_format.

The sequence of files should be stored with the pattern:
XXXXYYYY.ZZZ

where XXXX is a prefix, YYYY is a number, and .ZZZ is the extension of a known type
(either .hnd, .pfm, or .raw).

For example the following would be a good directory layout for pfm files:

Files/image_00.pfm
Files/image_00.txt
Files/image_01.pfm
Files/image_01.txt
etc...

The Varian hnd files should be stored in the original layout. For example:

Files/ProjectionInfo.xml
Files/Scan0/Proj_0000.hnd
Files/Scan0/Proj_0001.hnd
etc...

No geometry txt files are needed to reconstruct from Varian hnd format.

IMAGE GEOMETRY


By default, when you generate a DRR, the image is oriented as if the virtual x-ray source
were a camera. That means that for a right lateral film, the columns of the image go from
inf to sup, and the rows go from ant to post. The Varian OBI system produces HND files,
which are oriented differently. For a right lateral film, the columns of the HND images go
from ant to post, and the rows go from sup to inf. An illustration of this idea is shown
in the figure below.
[image] Geometry of Varian HND files.UNINDENT

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