Difference between revisions of "RTK/Examples/VarianReconstruction"

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(Created page with "== Varian Reconstruction == The first step before we can proceed with our reconstruction is to convert Varian's geometry into RTKs format using a command line tool. In order...")
 
 
(5 intermediate revisions by the same user not shown)
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== Varian Reconstruction ==
+
== Varian OBI Reconstruction ==
  
 
The first step before we can proceed with our reconstruction is to convert Varian's geometry into RTKs format using a command line tool.  
 
The first step before we can proceed with our reconstruction is to convert Varian's geometry into RTKs format using a command line tool.  
 
In order to carry out the reconstruction you just need to follow these simple steps:
 
In order to carry out the reconstruction you just need to follow these simple steps:
  
1. Download Varian dataset, [http://midas3.kitware.com/midas/download?items=32428 Varian-data]
+
1. Download Varian dataset, [https://data.kitware.com/api/v1/item/5be94de88d777f2179a24de0/download Varian-data]
  
 
2. Run the application to convert Varian's geometry into RTKs:
 
2. Run the application to convert Varian's geometry into RTKs:
 
      
 
      
   ./rtkvarianobigeometry --xml_file ProjectionInfo.xml --path Scan0/ --regexp Proj_.*.hnd -o varianGeometry
+
   rtkvarianobigeometry --xml_file ProjectionInfo.xml --path Scan0/ --regexp Proj_.*.hnd -o geometry.xml
  
 
3. Reconstruct varian-data using RTK applications such as rtkfdk algorithm. In this case we are going to reconstruct just a slice (30) of the whole volume:  
 
3. Reconstruct varian-data using RTK applications such as rtkfdk algorithm. In this case we are going to reconstruct just a slice (30) of the whole volume:  
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     --geometry geometry.xml \
 
     --geometry geometry.xml \
 
     --regexp .*.hnd \
 
     --regexp .*.hnd \
     --path ../Scan0 \
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     --path Scan0 \
 
     --output slice30.mha \
 
     --output slice30.mha \
 
     --verbose \
 
     --verbose \
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     --geometry geometry.xml \
 
     --geometry geometry.xml \
 
     --regexp .*.hnd \
 
     --regexp .*.hnd \
     --path ../Scan0 \
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     --path Scan0 \
 
     --reconstruction slice30.mha \
 
     --reconstruction slice30.mha \
 
     --output slice30.mha \
 
     --output slice30.mha \
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[[File:VarianSnapshot.jpg|400px]]
 
[[File:VarianSnapshot.jpg|400px]]
 +
 +
== Varian ProBeam Reconstruction ==
 +
 +
Similarly for the Varian ProBeam format:
 +
 +
1. Download a Varian ProBeam dataset, [https://data.kitware.com/api/v1/item/5be94bef8d777f2179a24ae1/download Varian-ProBeam-data]
 +
 +
2. Run the application to convert Varian ProBeam's geometry into RTKs:
 +
   
 +
  rtkvarianprobeamgeometry --xml_file Scan.xml --path Acquisitions/733061622 --regexp Proj_.*.xim -o geometry.xml
 +
 +
3. Reconstruct varian-data using RTK applications such as rtkfdk algorithm. In this case we are going to reconstruct just a slice (30) of the whole volume:
 +
 +
  rtkfdk \
 +
    --geometry geometry.xml \
 +
    --regexp .*.xim \
 +
    --path Acquisitions/733061622 \
 +
    --output slice58.mha \
 +
    --verbose \
 +
    --spacing 0.25,0.25,0.25 \
 +
    --dimension 1024,1,1024 \
 +
    --origin -127.875,-58,-127.875
 +
 +
4. We apply the FOV (field of view) filter, in order to discard everything that is outside our FOV:
 +
 +
  rtkfieldofview \
 +
    --geometry geometry.xml \
 +
    --regexp .*.xim \
 +
    --path Acquisitions/733061622 \
 +
    --reconstruction slice58.mha \
 +
    --output slice58.mha \
 +
    --verbose
 +
 +
5. Finally you can visualize your result with e.g. VV and it should look like the image below:
 +
 +
[[File:VarianSnapshotProBeam.jpg|400px]]

Latest revision as of 11:04, 12 November 2018

Varian OBI Reconstruction

The first step before we can proceed with our reconstruction is to convert Varian's geometry into RTKs format using a command line tool. In order to carry out the reconstruction you just need to follow these simple steps:

1. Download Varian dataset, Varian-data

2. Run the application to convert Varian's geometry into RTKs:

 rtkvarianobigeometry --xml_file ProjectionInfo.xml --path Scan0/ --regexp Proj_.*.hnd -o geometry.xml

3. Reconstruct varian-data using RTK applications such as rtkfdk algorithm. In this case we are going to reconstruct just a slice (30) of the whole volume:

 rtkfdk \
   --geometry geometry.xml \
   --regexp .*.hnd \
   --path Scan0 \
   --output slice30.mha \
   --verbose \
   --spacing 0.25,0.25,0.25 \
   --dimension 1024,1,1024 \
   --origin -127.875,30,-127.875

4. We apply the FOV (field of view) filter, in order to discard everything that is outside our FOV:

 rtkfieldofview \
   --geometry geometry.xml \
   --regexp .*.hnd \
   --path Scan0 \
   --reconstruction slice30.mha \
   --output slice30.mha \
   --verbose

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

VarianSnapshot.jpg

Varian ProBeam Reconstruction

Similarly for the Varian ProBeam format:

1. Download a Varian ProBeam dataset, Varian-ProBeam-data

2. Run the application to convert Varian ProBeam's geometry into RTKs:

 rtkvarianprobeamgeometry --xml_file Scan.xml --path Acquisitions/733061622 --regexp Proj_.*.xim -o geometry.xml

3. Reconstruct varian-data using RTK applications such as rtkfdk algorithm. In this case we are going to reconstruct just a slice (30) of the whole volume:

 rtkfdk \
   --geometry geometry.xml \
   --regexp .*.xim \
   --path Acquisitions/733061622 \
   --output slice58.mha \
   --verbose \
   --spacing 0.25,0.25,0.25 \
   --dimension 1024,1,1024 \
   --origin -127.875,-58,-127.875

4. We apply the FOV (field of view) filter, in order to discard everything that is outside our FOV:

 rtkfieldofview \
   --geometry geometry.xml \
   --regexp .*.xim \
   --path Acquisitions/733061622 \
   --reconstruction slice58.mha \
   --output slice58.mha \
   --verbose

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

VarianSnapshotProBeam.jpg