Varian Reconstruction¶

Varian OBI Reconstruction¶

The first step before proceeding with reconstruction is to convert Varian’s geometry into RTK’s format using a command-line tool. Follow these simple steps:

1. Download Varian Dataset¶

Download the dataset from Varian-data.

2. Convert Geometry¶

Run the application to convert Varian’s geometry into RTK’s format:

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

3. Reconstruct Using RTK Applications¶

Reconstruct a slice (e.g., slice 30) of the volume using the rtkfdk algorithm:

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. Apply the FOV Filter¶

Apply the field-of-view (FOV) filter to discard everything outside the FOV:

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

5. Visualize the Result¶

You can visualize the result using a viewer (e.g., VV). The resulting image should look like this:

Varian


Varian ProBeam Reconstruction¶

Follow these steps for the Varian ProBeam format:

1. Download Dataset¶

Download the dataset from Varian-ProBeam-data.

2. Convert Geometry¶

Run the application to convert Varian ProBeam’s geometry into RTK’s format:

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

3. Reconstruct Using RTK Applications¶

Reconstruct a slice (e.g., slice 58) of the volume using the rtkfdk algorithm:

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. Apply the FOV Filter¶

Apply the field-of-view (FOV) filter to discard everything outside the FOV:

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

5. Visualize the Result¶

You can visualize the result using a viewer (e.g., VV). The resulting image should look like this:

VarianProBeam