Elekta Reconstruction¶
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 individual 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.
Reconstruction Steps¶
The first step before proceeding with the reconstruction is to convert Elekta’s database information into an RTK geometry file using a command-line tool. Follow these steps:
1. Download Elekta Dataset¶
Download the dataset from Elekta-data.
2. Convert Geometry¶
Run the application to convert Elekta’s geometry into RTK’s format (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
Since XVI v5, the geometry is contained in a separate _Frames.xml
file, which can be used as follows:
rtkelektasynergygeometry \
--xml _Frames.xml \
-o elektaGeometry
An example of such a file is available in the test data here.
3. Reconstruct Using RTK Applications¶
Use the rtkfdk
algorithm to reconstruct a single axial slice (e.g., slice 29.5) of the volume:
rtkfdk \
--lowmem \
--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 Filter¶
Apply the field-of-view (FOV) filter to mask out everything outside the FOV:
rtkfieldofview \
--geometry elektaGeometry \
--path img_1.3.46.423632.135428.1351013645.166/ \
--regexp '.*.his' \
--reconstruction slice29.5.mha \
--output slice29.5.mha \
--verbose
5. Visualize the Result¶
You can visualize the result using a viewer (e.g., VV). The resulting image should look like the following: