RTK/Examples/ElektaReconstruction: Difference between revisions

From Openrtk
Jump to navigation Jump to search
No edit summary
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
== Elekta Data ==
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 invidual 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.
== Elekta Reconstruction ==
== Elekta Reconstruction ==


The first step before we can proceed with our reconstruction is to convert Elekta's geometry into RTKs format using a command line tool.  
The first step before one can proceed with the reconstruction is to convert Elekta's database information into RTK geometry file using a command line tool. This can be carried out following these steps:
In order to carry out the reconstruction you just need to follow these simple steps:


1. Download Elekta dataset, [http://midas3.kitware.com/midas/download?items=28897 Elekta-data]
1. Download Elekta dataset, [https://data.kitware.com/api/v1/item/5be973478d777f2179a26e1c/download Elekta-data]


2. Run the application to convert Elekta's geometry into RTKs:
2. Run the application to convert Elekta's geometry into RTKs (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
   rtkelektasynergygeometry \
    --image_db IMAGE.DBF \
    --frame_db FRAME.DBF \
    --dicom_uid 1.3.46.423632.135428.1351013645.166 \
    -o elektaGeometry


3. Reconstruct elekta-data using RTK applications such as rtkfdk algorithm. In this case we are going to reconstruct just a slice (29.5) of the whole volume:  
Note that since XVI v5, the geometry is contained in a separate _Frames.xml file which can be used with
 
  rtkelektasynergygeometry \
    --xml _Frames.xml \
    -o elektaGeometry
 
An example of such a file is available in our test data, [https://data.kitware.com/api/v1/item/5b179c898d777f15ebe201fd/download here].
 
3. Reconstruct elekta-data using RTK applications such as rtkfdk algorithm. In this case, we reconstruct just one axial slice (29.5) of the whole volume:  


   rtkfdk \
   rtkfdk \
    --lowmem \
     --geometry elektaGeometry \
     --geometry elektaGeometry \
     --path img_1.3.46.423632.135428.1351013645.166/ \
     --path img_1.3.46.423632.135428.1351013645.166/ \
Line 22: Line 40:
     --origin -127.875,29.5,-127.875
     --origin -127.875,29.5,-127.875


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


   rtkfieldofview \
   rtkfieldofview \
     --geometry geometry.xml \
     --geometry elektaGeometry \
     --path img_1.3.46.423632.135428.1351013645.166/ \
     --path img_1.3.46.423632.135428.1351013645.166/ \
     --regexp '.*.his' \
     --regexp '.*.his' \
Line 32: Line 50:
     --verbose
     --verbose


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


[[File:ElektaSnapshot.jpg|400px]]
[[File:ElektaSnapshot.jpg|400px]]

Latest revision as of 12:03, 12 November 2018

Elekta Data

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 invidual 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.

Elekta Reconstruction

The first step before one can proceed with the reconstruction is to convert Elekta's database information into RTK geometry file using a command line tool. This can be carried out following these steps:

1. Download Elekta dataset, Elekta-data

2. Run the application to convert Elekta's geometry into RTKs (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

Note that since XVI v5, the geometry is contained in a separate _Frames.xml file which can be used with

 rtkelektasynergygeometry \
   --xml _Frames.xml \
   -o elektaGeometry

An example of such a file is available in our test data, here.

3. Reconstruct elekta-data using RTK applications such as rtkfdk algorithm. In this case, we reconstruct just one axial slice (29.5) of the whole 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 (field of view) filter, in order to mask out everything that is 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. Finally, you can visualize the result (e.g. with VV) and it should look like the image below:

Error creating thumbnail: File missing