RTK/Examples/VarianReconstruction

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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