RTK/Scripts/ForwardProjection: Difference between revisions

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(Created page with "<div class="floatcenter">File:POPISinogram.pngFile:POPIReconstruction.png</div> This script uses the files [[http://www.creatis.insa-lyon.fr/~delmon/MedPhys11/bl/mhd/...")
 
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<div class="floatcenter">[[File:POPISinogram.png]][[File:POPIReconstruction.png]]</div>
<div class="floatcenter">[[File:POPISinogram.png|250px]][[File:POPIReconstruction.png|250px]]</div>


This script uses the files [[http://www.creatis.insa-lyon.fr/~delmon/MedPhys11/bl/mhd/00.mhd 00.mhd]] and [[http://www.creatis.insa-lyon.fr/~delmon/MedPhys11/bl/mhd/00.raw 00.raw]] of the [[http://www.creatis.insa-lyon.fr/rio/popi-model/ POPI]] as input.
This script uses the files [[http://www.creatis.insa-lyon.fr/~srit/POPI/MedPhys11/bl/mhd/00.mhd 00.mhd]] and [[http://www.creatis.insa-lyon.fr/~srit/POPI/MedPhys11/bl/mhd/00.raw 00.raw]] of the [[http://www.creatis.insa-lyon.fr/rio/popi-model/ POPI]] as input.


<source lang="bash">
<source lang="bash">
  # Create a simulated geometry
  # Create a simulated geometry
  rtksimulatedgeometry.exe -n 180 -o geometry.xml
  rtksimulatedgeometry -n 180 -o geometry.xml


  # Forward project
  # Forward project
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</source>
</source>


Note that the original file is in Hounsfield units which explain the negative values in the projection images since, e.g., the attenuation of air is -1000 HU. It is also worth of note that the file is oriented in the DICOM coordinate system although RTK uses the 61217 which results in a rotation around antero-posterior axis of the patient. This can be easily changed by modifying the TransformMatrix in the 00.mhd file.
Note that the original file is in Hounsfield units which explains the negative values in the projection images since, e.g., the attenuation of air is -1000 HU.
 
It is also worth of note that the file is oriented in the DICOM coordinate system although RTK uses the IEC 61217 which results in a rotation around the antero-posterior axis of the patient. This can be easily changed by modifying the TransformMatrix in the 00.mhd file.

Latest revision as of 07:19, 16 July 2015

Error creating thumbnail: File missing
Error creating thumbnail: File missing

This script uses the files [00.mhd] and [00.raw] of the [POPI] as input.

 # Create a simulated geometry
 rtksimulatedgeometry -n 180 -o geometry.xml

 # Forward project
 rtkforwardprojections -g geometry.xml -o projections.mha -i 00.mhd --spacing 2 --dimension 512

 # Reconstruct in the same resolution as the original
 rtkfdk -p . -r projections.mha -o fdk.mha -g geometry.xml --spacing=0.976562,0.976562,2 --origin=-250,-250,-164.5 --dimension=512,512,141

Note that the original file is in Hounsfield units which explains the negative values in the projection images since, e.g., the attenuation of air is -1000 HU.

It is also worth of note that the file is oriented in the DICOM coordinate system although RTK uses the IEC 61217 which results in a rotation around the antero-posterior axis of the patient. This can be easily changed by modifying the TransformMatrix in the 00.mhd file.