Difference between revisions of "RTK/Examples/ElektaReconstruction"

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== Elekta Data ==
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Elekta provides easy access to raw data. The data and projection images are stored in a single directory which is user configurable. The default location is D:\db. In this folder, there is a database in DBase format. Each table is contained in a .DBF file. RTK needs the IMAGE.DBF and FRAME.DBF tables.
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Patient data are stored in invidual folders. By default, the name of each patient folder is patient_ID where ID is the patient ID. In these folders, one can access the planning CT in the CT_SET subfolder and the cone-beam projections in IMAGES/img_DICOM_UID subfolders where DICOM_UID is the DICOM UID of the acquisition. The projection images are .his files. The reconstructed images are the IMAGES/img_DICOM_UID/Reconstruction/*SCAN files.
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== Elekta Reconstruction ==
 
== Elekta Reconstruction ==
  
The first step before we can proceed with our reconstruction is to convert Elekta's geometry into RTKs format using a command line tool.  
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The first step before one can proceed with the reconstruction is to convert Elekta's database information into RTK geometry file using a command line tool. This can be acrried out following these steps:
In order to carry out the reconstruction you just need to follow these simple steps:
 
  
 
1. Download Elekta dataset, [http://midas3.kitware.com/midas/download?items=28897 Elekta-data]
 
1. Download Elekta dataset, [http://midas3.kitware.com/midas/download?items=28897 Elekta-data]
  
2. Run the application to convert Elekta's geometry into RTKs:
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2. Run the application to convert Elekta's geometry into RTKs (DICOM_UID is contained in the subfolder name of the his files):
 
      
 
      
 
   rtkelektasynergygeometry --image_db IMAGE.DBF --frame_db FRAME.DBF --dicom_uid 1.3.46.423632.135428.1351013645.166 -o elektaGeometry
 
   rtkelektasynergygeometry --image_db IMAGE.DBF --frame_db FRAME.DBF --dicom_uid 1.3.46.423632.135428.1351013645.166 -o elektaGeometry
  
3. Reconstruct elekta-data using RTK applications such as rtkfdk algorithm. In this case we are going to reconstruct just a slice (29.5) of the whole volume:  
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3. Reconstruct elekta-data using RTK applications such as rtkfdk algorithm. In this case, we reconstruct just one axial slice (29.5) of the whole volume:  
  
 
   rtkfdk \
 
   rtkfdk \
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     --origin -127.875,29.5,-127.875
 
     --origin -127.875,29.5,-127.875
  
4. We apply the FOV (field of view) filter, in order to discard everything that is outside our FOV:
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4. Apply the FOV (field of view) filter, in order to mask out everything that is outside the FOV:
  
 
   rtkfieldofview \
 
   rtkfieldofview \
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     --verbose
 
     --verbose
  
5. Finally you can visualize your result with e.g. VV and it should look like the image below:
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5. Finally, you can visualize the result (e.g. with VV) and it should look like the image below:
  
 
[[File:ElektaSnapshot.jpg|400px]]
 
[[File:ElektaSnapshot.jpg|400px]]

Revision as of 05:23, 8 October 2013

Elekta Data

Elekta provides easy access to raw data. The data and projection images are stored in a single directory which is user configurable. The default location is D:\db. In this folder, there is a database in DBase format. Each table is contained in a .DBF file. RTK needs the IMAGE.DBF and FRAME.DBF tables.

Patient data are stored in invidual folders. By default, the name of each patient folder is patient_ID where ID is the patient ID. In these folders, one can access the planning CT in the CT_SET subfolder and the cone-beam projections in IMAGES/img_DICOM_UID subfolders where DICOM_UID is the DICOM UID of the acquisition. The projection images are .his files. The reconstructed images are the IMAGES/img_DICOM_UID/Reconstruction/*SCAN files.

Elekta Reconstruction

The first step before one can proceed with the reconstruction is to convert Elekta's database information into RTK geometry file using a command line tool. This can be acrried out following these steps:

1. Download Elekta dataset, Elekta-data

2. Run the application to convert Elekta's geometry into RTKs (DICOM_UID is contained in the subfolder name of the his files):

 rtkelektasynergygeometry --image_db IMAGE.DBF --frame_db FRAME.DBF --dicom_uid 1.3.46.423632.135428.1351013645.166 -o elektaGeometry

3. Reconstruct elekta-data using RTK applications such as rtkfdk algorithm. In this case, we reconstruct just one axial slice (29.5) of the whole volume:

 rtkfdk \
   --geometry elektaGeometry \
   --path img_1.3.46.423632.135428.1351013645.166/ \
   --regexp '.*.his' \
   --output slice29.5.mha \
   --verbose \
   --spacing 0.25,0.25,0.25 \
   --dimension 1024,1,1024 \
   --origin -127.875,29.5,-127.875

4. Apply the FOV (field of view) filter, in order to mask out everything that is outside the FOV:

 rtkfieldofview \
   --geometry geometry.xml \
   --path img_1.3.46.423632.135428.1351013645.166/ \
   --regexp '.*.his' \
   --reconstruction slice29.5.mha \
   --output slice29.5.mha \
   --verbose

5. Finally, you can visualize the result (e.g. with VV) and it should look like the image below:

ElektaSnapshot.jpg