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 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: